diff --git a/CHANGELOG.md b/CHANGELOG.md
index 543c2231ccbf..6ca671f23fcb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+
+### Bug Fixes
+
+* **deps:** update dependency escaya to ^0.0.49 ([#854](https://github.com/mikro-orm/mikro-orm/issues/854)) ([d4737b6](https://github.com/mikro-orm/mikro-orm/commit/d4737b646fe52c5bf4797312835cc974f4fe7b7c))
+* **migrations:** migrate only one version down with explicit tx ([50567dd](https://github.com/mikro-orm/mikro-orm/commit/50567ddd384ac2b53512925cade28e8debbb9f3b)), closes [#855](https://github.com/mikro-orm/mikro-orm/issues/855)
+* **query-builder:** do not select 1:1 owner when auto-joining ([86c3032](https://github.com/mikro-orm/mikro-orm/commit/86c303229c2ac7b77d245000f64562c0cc529320)), closes [#858](https://github.com/mikro-orm/mikro-orm/issues/858)
+* **query-builder:** fix auto-joining of 1:m PKs ([920995f](https://github.com/mikro-orm/mikro-orm/commit/920995f94070ff242b297d2837d83c7d9a9cb776)), closes [#857](https://github.com/mikro-orm/mikro-orm/issues/857)
+* **query-builder:** fix count query with auto-joining of 1:1 ([9b8056c](https://github.com/mikro-orm/mikro-orm/commit/9b8056c7440b836d22c8175ba90adf70fc3b052e)), closes [#858](https://github.com/mikro-orm/mikro-orm/issues/858)
+* **query-builder:** wrap nested array conditions with `$in` operator ([939989a](https://github.com/mikro-orm/mikro-orm/commit/939989add4f670deefe44f5a7faedb9b64155ba5)), closes [#860](https://github.com/mikro-orm/mikro-orm/issues/860)
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 
diff --git a/lerna.json b/lerna.json
index 088addd4f31f..0d65332e96b8 100644
--- a/lerna.json
+++ b/lerna.json
@@ -2,7 +2,7 @@
   "packages": [
     "packages/*"
   ],
-  "version": "4.0.5",
+  "version": "4.0.6",
   "command": {
     "version": {
       "conventionalCommits": true,
diff --git a/packages/cli/CHANGELOG.md b/packages/cli/CHANGELOG.md
index 014f85bbdbca..36eddbd53910 100644
--- a/packages/cli/CHANGELOG.md
+++ b/packages/cli/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/cli
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/cli
diff --git a/packages/cli/package.json b/packages/cli/package.json
index 9f794e2a38c1..5ad18eb37629 100644
--- a/packages/cli/package.json
+++ b/packages/cli/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/cli",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -50,10 +50,10 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/core": "^4.0.5",
-    "@mikro-orm/entity-generator": "^4.0.5",
-    "@mikro-orm/knex": "^4.0.5",
-    "@mikro-orm/migrations": "^4.0.5",
+    "@mikro-orm/core": "^4.0.6",
+    "@mikro-orm/entity-generator": "^4.0.6",
+    "@mikro-orm/knex": "^4.0.6",
+    "@mikro-orm/migrations": "^4.0.6",
     "ansi-colors": "^4.1.1",
     "cli-table3": "^0.6.0",
     "fs-extra": "^9.0.1",
diff --git a/packages/core/CHANGELOG.md b/packages/core/CHANGELOG.md
index 9560d5cb265e..617f5b2df600 100644
--- a/packages/core/CHANGELOG.md
+++ b/packages/core/CHANGELOG.md
@@ -3,6 +3,18 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+
+### Bug Fixes
+
+* **deps:** update dependency escaya to ^0.0.49 ([#854](https://github.com/mikro-orm/mikro-orm/issues/854)) ([d4737b6](https://github.com/mikro-orm/mikro-orm/commit/d4737b646fe52c5bf4797312835cc974f4fe7b7c))
+* **query-builder:** wrap nested array conditions with `$in` operator ([939989a](https://github.com/mikro-orm/mikro-orm/commit/939989add4f670deefe44f5a7faedb9b64155ba5)), closes [#860](https://github.com/mikro-orm/mikro-orm/issues/860)
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 
diff --git a/packages/core/package.json b/packages/core/package.json
index 78d34a2e7b06..64968e35ae52 100644
--- a/packages/core/package.json
+++ b/packages/core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/core",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -49,7 +49,7 @@
   "dependencies": {
     "ansi-colors": "^4.1.1",
     "clone": "^2.1.2",
-    "escaya": "^0.0.47",
+    "escaya": "^0.0.49",
     "fast-deep-equal": "^3.1.3",
     "fs-extra": "^9.0.1",
     "globby": "^11.0.1",
diff --git a/packages/core/src/utils/QueryHelper.ts b/packages/core/src/utils/QueryHelper.ts
index ceb25467c6ca..3ebf5fb739ee 100644
--- a/packages/core/src/utils/QueryHelper.ts
+++ b/packages/core/src/utils/QueryHelper.ts
@@ -73,7 +73,7 @@ export class QueryHelper {
     const meta = metadata.find(entityName);
 
     // inline PK-only objects in M:N queries so we don't join the target entity when not needed
-    if (meta) {
+    if (meta && root) {
       QueryHelper.inlinePrimaryKeyObjects(where as Dictionary, meta, metadata);
     }
 
@@ -87,7 +87,7 @@ export class QueryHelper {
       where = { [Utils.getPrimaryKeyHash(meta.primaryKeys)]: where };
     }
 
-    if (Array.isArray(where)) {
+    if (Array.isArray(where) && root) {
       const rootPrimaryKey = meta ? Utils.getPrimaryKeyHash(meta.primaryKeys) : entityName;
       return { [rootPrimaryKey]: { $in: (where as FilterQuery<T>[]).map(sub => QueryHelper.processWhere(sub, entityName, metadata, platform, convertCustomTypes, false)) } } as FilterQuery<T>;
     }
@@ -107,18 +107,27 @@ export class QueryHelper {
         return o;
       }
 
+      // wrap top level operators (except $not) with PK
+      if (Utils.isOperator(key) && root && meta && key !== '$not') {
+        const rootPrimaryKey = Utils.getPrimaryKeyHash(meta.primaryKeys);
+        o[rootPrimaryKey] = { [key]: QueryHelper.processWhere(value, entityName, metadata, platform, convertCustomTypes, false) };
+        return o;
+      }
+
       if (prop?.customType && convertCustomTypes) {
         value = QueryHelper.processCustomType(prop, value, platform, undefined, true);
       }
 
-      if (Array.isArray(value) && !QueryHelper.isSupportedOperator(key) && !key.includes('?')) {
+      if (Array.isArray(value) && !Utils.isOperator(key) && !QueryHelper.isSupportedOperator(key) && !key.includes('?')) {
         // comparing single composite key - use $eq instead of $in
         const op = !value.every(v => Array.isArray(v)) && composite ? '$eq' : '$in';
         o[key] = { [op]: value };
         return o;
       }
 
-      if (!QueryHelper.isSupportedOperator(key)) {
+      if (Utils.isPlainObject(value)) {
+        o[key] = QueryHelper.processWhere(value, prop?.type ?? entityName, metadata, platform, convertCustomTypes, false);
+      } else if (!QueryHelper.isSupportedOperator(key)) {
         o[key] = value;
       } else if (key.includes(':')) {
         const [k, expr] = key.split(':');
diff --git a/packages/entity-generator/CHANGELOG.md b/packages/entity-generator/CHANGELOG.md
index ec5a3127dfd9..ff851ea5d438 100644
--- a/packages/entity-generator/CHANGELOG.md
+++ b/packages/entity-generator/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/entity-generator
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/entity-generator
diff --git a/packages/entity-generator/package.json b/packages/entity-generator/package.json
index a240d5d43cde..6c579d7680c7 100644
--- a/packages/entity-generator/package.json
+++ b/packages/entity-generator/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/entity-generator",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,11 +47,11 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/knex": "^4.0.5",
+    "@mikro-orm/knex": "^4.0.6",
     "fs-extra": "^9.0.1"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/packages/knex/CHANGELOG.md b/packages/knex/CHANGELOG.md
index a7b1e7255688..448ae57d92e7 100644
--- a/packages/knex/CHANGELOG.md
+++ b/packages/knex/CHANGELOG.md
@@ -3,6 +3,20 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+
+### Bug Fixes
+
+* **query-builder:** do not select 1:1 owner when auto-joining ([86c3032](https://github.com/mikro-orm/mikro-orm/commit/86c303229c2ac7b77d245000f64562c0cc529320)), closes [#858](https://github.com/mikro-orm/mikro-orm/issues/858)
+* **query-builder:** fix auto-joining of 1:m PKs ([920995f](https://github.com/mikro-orm/mikro-orm/commit/920995f94070ff242b297d2837d83c7d9a9cb776)), closes [#857](https://github.com/mikro-orm/mikro-orm/issues/857)
+* **query-builder:** fix count query with auto-joining of 1:1 ([9b8056c](https://github.com/mikro-orm/mikro-orm/commit/9b8056c7440b836d22c8175ba90adf70fc3b052e)), closes [#858](https://github.com/mikro-orm/mikro-orm/issues/858)
+* **query-builder:** wrap nested array conditions with `$in` operator ([939989a](https://github.com/mikro-orm/mikro-orm/commit/939989add4f670deefe44f5a7faedb9b64155ba5)), closes [#860](https://github.com/mikro-orm/mikro-orm/issues/860)
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 
diff --git a/packages/knex/package.json b/packages/knex/package.json
index d6f4a829c825..88048458d630 100644
--- a/packages/knex/package.json
+++ b/packages/knex/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/knex",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -51,7 +51,7 @@
     "knex": "^0.21.1"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0",
diff --git a/packages/knex/src/query/QueryBuilder.ts b/packages/knex/src/query/QueryBuilder.ts
index d238a98505b8..bfb49c80e38c 100644
--- a/packages/knex/src/query/QueryBuilder.ts
+++ b/packages/knex/src/query/QueryBuilder.ts
@@ -60,6 +60,10 @@ export class QueryBuilder<T extends AnyEntity<T> = AnyEntity> {
   }
 
   addSelect(fields: string | string[]): this {
+    if (this.type && this.type !== QueryType.SELECT) {
+      return this;
+    }
+
     return this.select([...Utils.asArray(this._fields), ...Utils.asArray(fields)]);
   }
 
diff --git a/packages/knex/src/query/QueryBuilderHelper.ts b/packages/knex/src/query/QueryBuilderHelper.ts
index 47d09d7d1432..fc637e19ad84 100644
--- a/packages/knex/src/query/QueryBuilderHelper.ts
+++ b/packages/knex/src/query/QueryBuilderHelper.ts
@@ -311,11 +311,6 @@ export class QueryBuilderHelper {
     const replacement = this.getOperatorReplacement(op, value);
     const fields = Utils.splitPrimaryKeys(key);
 
-    if (key === op) { // substitute top level operators with PK
-      const meta = this.metadata.find(this.entityName)!;
-      key = meta.properties[meta.primaryKeys[0]].fieldNames[0];
-    }
-
     if (fields.length > 1 && Array.isArray(value[op]) && !value[op].every((v: unknown) => Array.isArray(v))) {
       value[op] = this.knex.raw(`(${fields.map(() => '?').join(', ')})`, value[op]);
     }
diff --git a/packages/knex/src/query/ScalarCriteriaNode.ts b/packages/knex/src/query/ScalarCriteriaNode.ts
index 41df849fca00..9e15f5ba7af0 100644
--- a/packages/knex/src/query/ScalarCriteriaNode.ts
+++ b/packages/knex/src/query/ScalarCriteriaNode.ts
@@ -6,16 +6,19 @@ export class ScalarCriteriaNode extends CriteriaNode {
 
   process<T>(qb: IQueryBuilder<T>, alias?: string): any {
     if (this.shouldJoin()) {
-      const nestedAlias = qb.getAliasForJoinPath(this.getPath()) || qb.getNextAlias();
+      const path = this.getPath();
+      const parentPath = this.parent ? this.parent.getPath() : path;
+      const nestedAlias = qb.getAliasForJoinPath(path) || qb.getNextAlias();
       const field = `${alias}.${this.prop!.name}`;
 
       if (this.prop!.reference === ReferenceType.MANY_TO_MANY) {
-        qb.join(field, nestedAlias, undefined, 'pivotJoin', this.getPath());
+        qb.join(field, nestedAlias, undefined, 'pivotJoin', path);
       } else {
-        qb.join(field, nestedAlias, undefined, 'leftJoin', this.getPath());
+        qb.join(field, nestedAlias, undefined, 'leftJoin', path);
       }
 
-      if (this.prop!.reference === ReferenceType.ONE_TO_ONE) {
+      // select the owner as virtual property when joining from 1:1 inverse side, but only if the parent is root entity
+      if (this.prop!.reference === ReferenceType.ONE_TO_ONE && !parentPath.includes('.')) {
         qb.addSelect(field);
       }
     }
@@ -24,15 +27,16 @@ export class ScalarCriteriaNode extends CriteriaNode {
   }
 
   shouldJoin(): boolean {
-    if (!this.parent || !this.prop || [ReferenceType.SCALAR, ReferenceType.ONE_TO_MANY].includes(this.prop.reference)) {
+    if (!this.parent || !this.prop) {
       return false;
     }
 
-    if (this.prop.reference === ReferenceType.ONE_TO_ONE) {
-      return !this.prop.owner;
+    switch (this.prop.reference) {
+      case ReferenceType.ONE_TO_MANY: return true;
+      case ReferenceType.MANY_TO_MANY: return true;
+      case ReferenceType.ONE_TO_ONE: return !this.prop.owner;
+      default: return false; // SCALAR, MANY_TO_ONE
     }
-
-    return this.prop.reference === ReferenceType.MANY_TO_MANY;
   }
 
 }
diff --git a/packages/mariadb/CHANGELOG.md b/packages/mariadb/CHANGELOG.md
index a33018106222..5763769774af 100644
--- a/packages/mariadb/CHANGELOG.md
+++ b/packages/mariadb/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/mariadb
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/mariadb
diff --git a/packages/mariadb/package.json b/packages/mariadb/package.json
index 54b2e5ca6a09..e00efd4f7c24 100644
--- a/packages/mariadb/package.json
+++ b/packages/mariadb/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/mariadb",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,11 +47,11 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/mysql-base": "^4.0.5",
+    "@mikro-orm/mysql-base": "^4.0.6",
     "mariadb": "^2.4.0"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/packages/migrations/CHANGELOG.md b/packages/migrations/CHANGELOG.md
index 1cff8fd8dc19..077a7bc4a876 100644
--- a/packages/migrations/CHANGELOG.md
+++ b/packages/migrations/CHANGELOG.md
@@ -3,6 +3,17 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+
+### Bug Fixes
+
+* **migrations:** migrate only one version down with explicit tx ([50567dd](https://github.com/mikro-orm/mikro-orm/commit/50567ddd384ac2b53512925cade28e8debbb9f3b)), closes [#855](https://github.com/mikro-orm/mikro-orm/issues/855)
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/migrations
diff --git a/packages/migrations/package.json b/packages/migrations/package.json
index 56e7202496a8..fa3c0b65a533 100644
--- a/packages/migrations/package.json
+++ b/packages/migrations/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/migrations",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,13 +47,13 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/knex": "^4.0.5",
+    "@mikro-orm/knex": "^4.0.6",
     "@types/umzug": "^2.2.3",
     "fs-extra": "^9.0.1",
     "umzug": "^2.3.0"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/packages/migrations/src/Migrator.ts b/packages/migrations/src/Migrator.ts
index d94a36d134fd..e28be7966e8a 100644
--- a/packages/migrations/src/Migrator.ts
+++ b/packages/migrations/src/Migrator.ts
@@ -134,12 +134,12 @@ export class Migrator {
     return lines;
   }
 
-  private prefix<T extends string | string[] | { from?: string; to?: string; migrations?: string[] }>(options?: T): T {
+  private prefix<T extends string | string[] | { from?: string; to?: string; migrations?: string[]; transaction?: Transaction }>(options?: T): T {
     if (Utils.isString(options) || Array.isArray(options)) {
       return Utils.asArray(options).map(m => m.startsWith('Migration') ? m : 'Migration' + m) as T;
     }
 
-    if (!Utils.isObject<{ from?: string; to?: string; migrations?: string[] }>(options)) {
+    if (!Utils.isObject<{ from?: string; to?: string; migrations?: string[]; transaction?: Transaction }>(options)) {
       return options as T;
     }
 
@@ -147,6 +147,10 @@ export class Migrator {
       options.migrations = options.migrations.map(m => this.prefix(m));
     }
 
+    if (options.transaction) {
+      delete options.transaction;
+    }
+
     ['from', 'to'].filter(k => options[k]).forEach(k => options[k] = this.prefix(options[k]));
 
     return options as T;
diff --git a/packages/mikro-orm/CHANGELOG.md b/packages/mikro-orm/CHANGELOG.md
index 95953c96b918..29d2cb546b1e 100644
--- a/packages/mikro-orm/CHANGELOG.md
+++ b/packages/mikro-orm/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package mikro-orm
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package mikro-orm
diff --git a/packages/mikro-orm/package.json b/packages/mikro-orm/package.json
index 1a786b43afa9..4e0d63946a33 100644
--- a/packages/mikro-orm/package.json
+++ b/packages/mikro-orm/package.json
@@ -1,6 +1,6 @@
 {
   "name": "mikro-orm",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,11 +47,11 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/cli": "^4.0.5",
-    "@mikro-orm/core": "^4.0.5",
-    "@mikro-orm/entity-generator": "^4.0.5",
-    "@mikro-orm/migrations": "^4.0.5",
-    "@mikro-orm/reflection": "^4.0.5"
+    "@mikro-orm/cli": "^4.0.6",
+    "@mikro-orm/core": "^4.0.6",
+    "@mikro-orm/entity-generator": "^4.0.6",
+    "@mikro-orm/migrations": "^4.0.6",
+    "@mikro-orm/reflection": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/mariadb": "^4.0.0",
diff --git a/packages/mongodb/CHANGELOG.md b/packages/mongodb/CHANGELOG.md
index 4e1bdc137d26..98e2ea58f172 100644
--- a/packages/mongodb/CHANGELOG.md
+++ b/packages/mongodb/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/mongodb
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/mongodb
diff --git a/packages/mongodb/package.json b/packages/mongodb/package.json
index 271702b384f0..47616e1d17ad 100644
--- a/packages/mongodb/package.json
+++ b/packages/mongodb/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/mongodb",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -51,7 +51,7 @@
     "mongodb": "^3.6.0"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/packages/mysql-base/CHANGELOG.md b/packages/mysql-base/CHANGELOG.md
index 384bfa33b736..f1d7b258b39b 100644
--- a/packages/mysql-base/CHANGELOG.md
+++ b/packages/mysql-base/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/mysql-base
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/mysql-base
diff --git a/packages/mysql-base/package.json b/packages/mysql-base/package.json
index a92eaada7d29..0af3eb3c771c 100644
--- a/packages/mysql-base/package.json
+++ b/packages/mysql-base/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/mysql-base",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,10 +47,10 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/knex": "^4.0.5"
+    "@mikro-orm/knex": "^4.0.6"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0",
diff --git a/packages/mysql/CHANGELOG.md b/packages/mysql/CHANGELOG.md
index 4660672a5c55..6d8112957007 100644
--- a/packages/mysql/CHANGELOG.md
+++ b/packages/mysql/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/mysql
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/mysql
diff --git a/packages/mysql/package.json b/packages/mysql/package.json
index 1fbac10db460..b076f1e491a4 100644
--- a/packages/mysql/package.json
+++ b/packages/mysql/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/mysql",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,11 +47,11 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/mysql-base": "^4.0.5",
-    "mysql2": "sidorares/node-mysql2#master"
+    "@mikro-orm/mysql-base": "^4.0.6",
+    "mysql2": "^2.2.5"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/packages/postgresql/CHANGELOG.md b/packages/postgresql/CHANGELOG.md
index 0e75501eb190..972396a66b38 100644
--- a/packages/postgresql/CHANGELOG.md
+++ b/packages/postgresql/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/postgresql
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 
diff --git a/packages/postgresql/package.json b/packages/postgresql/package.json
index c083bead7e17..46e4e33a1c35 100644
--- a/packages/postgresql/package.json
+++ b/packages/postgresql/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/postgresql",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,11 +47,11 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/knex": "^4.0.5",
+    "@mikro-orm/knex": "^4.0.6",
     "pg": "^8.2.1"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/packages/reflection/CHANGELOG.md b/packages/reflection/CHANGELOG.md
index 7535b8a11159..e702dab8a8b6 100644
--- a/packages/reflection/CHANGELOG.md
+++ b/packages/reflection/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/reflection
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 **Note:** Version bump only for package @mikro-orm/reflection
diff --git a/packages/reflection/package.json b/packages/reflection/package.json
index 1c6195918d2f..4287a7bdfa36 100644
--- a/packages/reflection/package.json
+++ b/packages/reflection/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/reflection",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -51,7 +51,7 @@
     "ts-morph": "^8.0.0"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/packages/sqlite/CHANGELOG.md b/packages/sqlite/CHANGELOG.md
index 2c9cfa66e638..2d2f7076656f 100644
--- a/packages/sqlite/CHANGELOG.md
+++ b/packages/sqlite/CHANGELOG.md
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.0.6](https://github.com/mikro-orm/mikro-orm/compare/v4.0.5...v4.0.6) (2020-09-22)
+
+**Note:** Version bump only for package @mikro-orm/sqlite
+
+
+
+
+
 ## [4.0.5](https://github.com/mikro-orm/mikro-orm/compare/v4.0.4...v4.0.5) (2020-09-21)
 
 
diff --git a/packages/sqlite/package.json b/packages/sqlite/package.json
index 86aa971c8f8b..c06b30f086e6 100644
--- a/packages/sqlite/package.json
+++ b/packages/sqlite/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mikro-orm/sqlite",
-  "version": "4.0.5",
+  "version": "4.0.6",
   "description": "TypeScript ORM for Node.js based on Data Mapper, Unit of Work and Identity Map patterns. Supports MongoDB, MySQL, PostgreSQL and SQLite databases as well as usage with vanilla JavaScript.",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
@@ -47,12 +47,12 @@
     "access": "public"
   },
   "dependencies": {
-    "@mikro-orm/knex": "^4.0.5",
+    "@mikro-orm/knex": "^4.0.6",
     "fs-extra": "^9.0.1",
     "sqlite3": "^4.2.0"
   },
   "devDependencies": {
-    "@mikro-orm/core": "^4.0.5"
+    "@mikro-orm/core": "^4.0.6"
   },
   "peerDependencies": {
     "@mikro-orm/core": "^4.0.0"
diff --git a/tests/EntityGenerator.test.ts b/tests/EntityGenerator.test.ts
index e2f5fb92b624..2c4ff9c793ac 100644
--- a/tests/EntityGenerator.test.ts
+++ b/tests/EntityGenerator.test.ts
@@ -6,7 +6,7 @@ import { initORMMySql, initORMPostgreSql, initORMSqlite } from './bootstrap';
 describe('EntityGenerator', () => {
 
   test('generate entities from schema [mysql]', async () => {
-    const orm = await initORMMySql();
+    const orm = await initORMMySql('mysql', {}, true);
     const generator = orm.getEntityGenerator();
     const dump = await generator.generate({ save: true, baseDir: './temp/entities' });
     expect(dump).toMatchSnapshot('mysql-entity-dump');
diff --git a/tests/Migrator.test.ts b/tests/Migrator.test.ts
index 43236769404f..a9a571e997b5 100644
--- a/tests/Migrator.test.ts
+++ b/tests/Migrator.test.ts
@@ -3,7 +3,7 @@ import umzug from 'umzug';
 import { Logger, MikroORM } from '@mikro-orm/core';
 import { Migration, MigrationStorage, Migrator } from '@mikro-orm/migrations';
 import { MySqlDriver } from '@mikro-orm/mysql';
-import { remove, writeFile } from 'fs-extra';
+import { remove } from 'fs-extra';
 import { initORMMySql } from './bootstrap';
 
 class MigrationTest1 extends Migration {
@@ -120,7 +120,9 @@ describe('Migrator', () => {
     await migrator.up();
     expect(upMock).toBeCalledTimes(1);
     expect(downMock).toBeCalledTimes(0);
-    await migrator.down();
+    await orm.em.begin();
+    await migrator.down({ transaction: orm.em.getTransactionContext() });
+    await orm.em.commit();
     expect(upMock).toBeCalledTimes(1);
     expect(downMock).toBeCalledTimes(1);
     upMock.mockRestore();
@@ -224,20 +226,34 @@ describe('Migrator', () => {
     const migrator = new Migrator(orm.em);
     const path = process.cwd() + '/temp/migrations';
 
-    const migration = await migrator.createMigration(path, true);
-    const migratorMock = jest.spyOn(Migration.prototype, 'down');
-    migratorMock.mockImplementation(async () => void 0);
+    // @ts-ignore
+    migrator.options.disableForeignKeys = false;
+
+    const dateMock = jest.spyOn(Date.prototype, 'toISOString');
+    dateMock.mockReturnValueOnce('2020-09-22T10:00:01.000Z');
+    dateMock.mockReturnValueOnce('2020-09-22T10:00:02.000Z');
+    const migration1 = await migrator.createMigration(path, true);
+    const migration2 = await migrator.createMigration(path, true);
+    const migrationMock = jest.spyOn(Migration.prototype, 'down');
+    migrationMock.mockImplementation(async () => void 0);
 
     const mock = jest.fn();
     const logger = new Logger(mock, ['query']);
     Object.assign(orm.config, { logger });
 
     await orm.em.transactional(async em => {
-      await migrator.up({ transaction: em.getTransactionContext() });
-      await migrator.down({ transaction: em.getTransactionContext() });
+      const ret1 = await migrator.up({ transaction: em.getTransactionContext() });
+      const ret2 = await migrator.down({ transaction: em.getTransactionContext() });
+      const ret3 = await migrator.down({ transaction: em.getTransactionContext() });
+      const ret4 = await migrator.down({ transaction: em.getTransactionContext() });
+      expect(ret1).toHaveLength(2);
+      expect(ret2).toHaveLength(1);
+      expect(ret3).toHaveLength(1);
+      expect(ret4).toHaveLength(0);
     });
 
-    await remove(path + '/' + migration.fileName);
+    await remove(path + '/' + migration1.fileName);
+    await remove(path + '/' + migration2.fileName);
     const calls = mock.mock.calls.map(call => {
       return call[0]
         .replace(/ \[took \d+ ms]/, '')
@@ -257,7 +273,6 @@ describe('Migrator', () => {
     const path = process.cwd() + '/temp/migrations';
 
     const migration = await migrator.createMigration(path, true);
-    await writeFile(path + '/' + migration.fileName, migration.code.replace(`'mikro-orm'`, `'@mikro-orm/migrations'`));
     const migratorMock = jest.spyOn(Migration.prototype, 'down');
     migratorMock.mockImplementation(async () => void 0);
 
diff --git a/tests/QueryBuilder.test.ts b/tests/QueryBuilder.test.ts
index 613666621a2d..f4709a314249 100644
--- a/tests/QueryBuilder.test.ts
+++ b/tests/QueryBuilder.test.ts
@@ -7,6 +7,7 @@ import { Address2, Author2, Book2, BookTag2, Car2, CarOwner2, Configuration2, Fo
 import { initORMMySql } from './bootstrap';
 import { BaseEntity2 } from './entities-sql/BaseEntity2';
 import { performance } from 'perf_hooks';
+import { BaseEntity22 } from './entities-sql/BaseEntity22';
 
 describe('QueryBuilder', () => {
 
@@ -1579,7 +1580,7 @@ describe('QueryBuilder', () => {
 
   test('pg array operators', async () => {
     const pg = await MikroORM.init<PostgreSqlDriver>({
-      entities: [Author2, Address2, Book2, BookTag2, Publisher2, Test2, BaseEntity2, Configuration2],
+      entities: [Author2, Address2, Book2, BookTag2, Publisher2, Test2, FooBar2, FooBaz2, BaseEntity2, BaseEntity22, Configuration2],
       dbName: `mikro_orm_test`,
       type: 'postgresql',
     });
@@ -1653,6 +1654,66 @@ describe('QueryBuilder', () => {
     expect(sql7).toBe('select `e0`.* from `test2` as `e0` where `e0`.`book_uuid_pk` in (?)');
   });
 
+  test('query by 1:m PK (GH issue 857)', async () => {
+    const sql0 = orm.em.createQueryBuilder(Author2).select('*').where({ books: '123' }).getQuery();
+    expect(sql0).toBe('select `e0`.* from `author2` as `e0` left join `book2` as `e1` on `e0`.`id` = `e1`.`author_id` where `e1`.`uuid_pk` = ?');
+    const expected = 'select `e0`.* from `author2` as `e0` left join `book2` as `e1` on `e0`.`id` = `e1`.`author_id` where `e1`.`uuid_pk` in (?)';
+    const sql1 = orm.em.createQueryBuilder(Author2).where({ books: [123] }).getQuery();
+    expect(sql1).toBe(expected);
+    const sql2 = orm.em.createQueryBuilder(Author2).where({ books: { uuid: [123] } }).getQuery();
+    expect(sql2).toBe(expected);
+    const sql3 = orm.em.createQueryBuilder(Author2).where({ books: { uuid: { $in: [123] } } }).getQuery();
+    expect(sql3).toBe(expected);
+    const sql4 = orm.em.createQueryBuilder(Author2).where({ $and: [{ books: { uuid: { $in: [123] } } }] }).getQuery();
+    expect(sql4).toBe(expected);
+    const sql5 = orm.em.createQueryBuilder(Author2).where({ $and: [{ books: [123] }] }).getQuery();
+    expect(sql5).toBe(expected);
+    const sql6 = orm.em.createQueryBuilder(Author2).where({ $and: [{ books: { uuid: [123] } }] }).getQuery();
+    expect(sql6).toBe(expected);
+  });
+
+  test('count query with auto-joining (GH issue 858)', async () => {
+    // m:1 -> 1:1 inverse -> PK
+    const sql1 = orm.em.createQueryBuilder(Author2).count().where({ favouriteBook: { test: { id: 1 } } }).getQuery();
+    expect(sql1).toBe('select count(`e0`.`id`) as `count` ' +
+      'from `author2` as `e0` ' +
+      'left join `book2` as `e1` on `e0`.`favourite_book_uuid_pk` = `e1`.`uuid_pk` ' +
+      'left join `test2` as `e2` on `e1`.`uuid_pk` = `e2`.`book_uuid_pk` ' +
+      'where `e2`.`id` = ?');
+
+    const sql2 = orm.em.createQueryBuilder(Author2).select('*').where({ favouriteBook: { test: { id: 1 } } }).getQuery();
+    expect(sql2).toBe('select `e0`.* ' +
+      'from `author2` as `e0` ' +
+      'left join `book2` as `e1` on `e0`.`favourite_book_uuid_pk` = `e1`.`uuid_pk` ' +
+      'left join `test2` as `e2` on `e1`.`uuid_pk` = `e2`.`book_uuid_pk` ' +
+      'where `e2`.`id` = ?');
+
+    const sql3 = orm.em.createQueryBuilder(Book2).count().where({ test: { id: 1 } }).getQuery();
+    expect(sql3).toBe('select count(`e0`.`uuid_pk`) as `count` ' +
+      'from `book2` as `e0` ' +
+      'left join `test2` as `e1` on `e0`.`uuid_pk` = `e1`.`book_uuid_pk` ' +
+      'where `e1`.`id` = ?');
+
+    const sql4 = orm.em.createQueryBuilder(Book2).select('*').where({ test: { id: 1 } }).getQuery();
+    expect(sql4).toBe('select `e0`.*, `e1`.`id` as `test_id`, `e0`.price * 1.19 as `price_taxed` ' +
+      'from `book2` as `e0` ' +
+      'left join `test2` as `e1` on `e0`.`uuid_pk` = `e1`.`book_uuid_pk` ' +
+      'where `e1`.`id` = ?');
+  });
+
+  test('deeply nested array condition without operator (GH issue 860)', async () => {
+    // 1:1 inverse -> m:n inverse -> [PK]
+    let expected = 'select `e0`.* from `foo_baz2` as `e0` left join `foo_bar2` as `e1` on `e0`.`id` = `e1`.`baz_id` left join `test2_bars` as `e2` on `e1`.`id` = `e2`.`foo_bar2_id` where `e2`.`test2_id` in (?, ?, ?)';
+    const sql1 = orm.em.createQueryBuilder(FooBaz2).where({ bar: { tests: { $in: [1, 2, 3] } } }).getQuery();
+    expect(sql1).toBe(expected);
+    const sql2 = orm.em.createQueryBuilder(FooBaz2).where({ bar: { tests: [1, 2, 3] } }).getQuery();
+    expect(sql2).toBe(expected);
+
+    expected = 'select `e0`.* from `foo_baz2` as `e0` left join `foo_bar2` as `e1` on `e0`.`id` = `e1`.`baz_id` left join `test2_bars` as `e2` on `e1`.`id` = `e2`.`foo_bar2_id` where `e2`.`test2_id` = ?';
+    const sql3 = orm.em.createQueryBuilder(FooBaz2).where({ bar: { tests: 3 } }).getQuery();
+    expect(sql3).toBe(expected);
+  });
+
   afterAll(async () => orm.close(true));
 
 });
diff --git a/tests/SchemaGenerator.test.ts b/tests/SchemaGenerator.test.ts
index 090013321a63..230f2666e2a6 100644
--- a/tests/SchemaGenerator.test.ts
+++ b/tests/SchemaGenerator.test.ts
@@ -1,15 +1,16 @@
 import { BASE_DIR, initORMMySql, initORMPostgreSql, initORMSqlite, initORMSqlite2 } from './bootstrap';
 import { EntitySchema, ReferenceType, Utils, MikroORM } from '@mikro-orm/core';
 import { SchemaGenerator, EntityManager } from '@mikro-orm/knex';
-import { FooBar2, FooBaz2 } from './entities-sql';
+import { Address2, Author2, Book2, BookTag2, Configuration2, FooBar2, FooBaz2, Publisher2, Test2 } from './entities-sql';
 import { BaseEntity22 } from './entities-sql/BaseEntity22';
+import { BaseEntity2 } from './entities-sql/BaseEntity2';
 
 describe('SchemaGenerator', () => {
 
   test('create/drop database [mysql]', async () => {
     const dbName = `mikro_orm_test_${Date.now()}`;
     const orm = await MikroORM.init({
-      entities: [FooBar2, FooBaz2, BaseEntity22],
+      entities: [FooBar2, FooBaz2, Test2, Book2, Author2, Configuration2, Publisher2, BookTag2, Address2, BaseEntity2, BaseEntity22],
       dbName,
       port: 3307,
       baseDir: BASE_DIR,
@@ -25,7 +26,7 @@ describe('SchemaGenerator', () => {
   test('create schema also creates the database if not exists [mysql]', async () => {
     const dbName = `mikro_orm_test_${Date.now()}`;
     const orm = await MikroORM.init({
-      entities: [FooBar2, FooBaz2, BaseEntity22],
+      entities: [FooBar2, FooBaz2, Test2, Book2, Author2, Configuration2, Publisher2, BookTag2, Address2, BaseEntity2, BaseEntity22],
       dbName,
       port: 3307,
       baseDir: BASE_DIR,
@@ -44,7 +45,7 @@ describe('SchemaGenerator', () => {
   test('create/drop database [mariadb]', async () => {
     const dbName = `mikro_orm_test_${Date.now()}`;
     const orm = await MikroORM.init({
-      entities: [FooBar2, FooBaz2, BaseEntity22],
+      entities: [FooBar2, FooBaz2, Test2, Book2, Author2, Configuration2, Publisher2, BookTag2, Address2, BaseEntity2, BaseEntity22],
       dbName,
       port: 3307,
       baseDir: BASE_DIR,
@@ -61,7 +62,7 @@ describe('SchemaGenerator', () => {
   test('create schema also creates the database if not exists [mariadb]', async () => {
     const dbName = `mikro_orm_test_${Date.now()}`;
     const orm = await MikroORM.init({
-      entities: [FooBar2, FooBaz2, BaseEntity22],
+      entities: [FooBar2, FooBaz2, Test2, Book2, Author2, Configuration2, Publisher2, BookTag2, Address2, BaseEntity2, BaseEntity22],
       dbName,
       port: 3307,
       baseDir: BASE_DIR,
@@ -378,7 +379,7 @@ describe('SchemaGenerator', () => {
   test('create/drop database [postgresql]', async () => {
     const dbName = `mikro_orm_test_${Date.now()}`;
     const orm = await MikroORM.init({
-      entities: [FooBar2, FooBaz2, BaseEntity22],
+      entities: [FooBar2, FooBaz2, Test2, Book2, Author2, Configuration2, Publisher2, BookTag2, Address2, BaseEntity2, BaseEntity22],
       dbName,
       baseDir: BASE_DIR,
       type: 'postgresql',
@@ -393,7 +394,7 @@ describe('SchemaGenerator', () => {
   test('create schema also creates the database if not exists [postgresql]', async () => {
     const dbName = `mikro_orm_test_${Date.now()}`;
     const orm = await MikroORM.init({
-      entities: [FooBar2, FooBaz2, BaseEntity22],
+      entities: [FooBar2, FooBaz2, Test2, Book2, Author2, Configuration2, Publisher2, BookTag2, Address2, BaseEntity2, BaseEntity22],
       dbName,
       baseDir: BASE_DIR,
       type: 'postgresql',
diff --git a/tests/__snapshots__/EntityGenerator.test.ts.snap b/tests/__snapshots__/EntityGenerator.test.ts.snap
index ae6110df4b8e..2cf51a3f22b9 100644
--- a/tests/__snapshots__/EntityGenerator.test.ts.snap
+++ b/tests/__snapshots__/EntityGenerator.test.ts.snap
@@ -437,6 +437,21 @@ export class Test2 {
   @Property({ fieldName: 'foo___baz', nullable: true })
   fooBaz?: number;
 
+}
+",
+  "import { Cascade, Entity, ManyToOne } from '@mikro-orm/core';
+import { FooBar2 } from './FooBar2';
+import { Test2 } from './Test2';
+
+@Entity()
+export class Test2Bars {
+
+  @ManyToOne({ entity: () => Test2, cascade: [Cascade.ALL], primary: true, index: 'test2_bars_test2_id_index' })
+  test2!: Test2;
+
+  @ManyToOne({ entity: () => FooBar2, cascade: [Cascade.ALL], primary: true, index: 'test2_bars_foo_bar2_id_index' })
+  fooBar2!: FooBar2;
+
 }
 ",
   "import { Entity, OneToOne, PrimaryKey, Property } from '@mikro-orm/core';
@@ -842,6 +857,21 @@ export class Test2 {
   @Property({ columnType: 'polygon', nullable: true })
   path?: string;
 
+}
+",
+  "import { Cascade, Entity, ManyToOne } from '@mikro-orm/core';
+import { FooBar2 } from './FooBar2';
+import { Test2 } from './Test2';
+
+@Entity()
+export class Test2Bars {
+
+  @ManyToOne({ entity: () => Test2, cascade: [Cascade.ALL], primary: true })
+  test2!: Test2;
+
+  @ManyToOne({ entity: () => FooBar2, cascade: [Cascade.ALL], primary: true })
+  fooBar2!: FooBar2;
+
 }
 ",
 ]
diff --git a/tests/__snapshots__/Migrator.test.ts.snap b/tests/__snapshots__/Migrator.test.ts.snap
index f24f2f2deea5..4bb3a120f394 100644
--- a/tests/__snapshots__/Migrator.test.ts.snap
+++ b/tests/__snapshots__/Migrator.test.ts.snap
@@ -94,6 +94,11 @@ export class Migration20191013214813 extends Migration {
     this.addSql('alter table \`publisher2_tests\` add index \`publisher2_tests_publisher2_id_index\`(\`publisher2_id\`);');
     this.addSql('alter table \`publisher2_tests\` add index \`publisher2_tests_test2_id_index\`(\`test2_id\`);');
 
+    this.addSql('create table \`test2_bars\` (\`test2_id\` int(11) unsigned not null, \`foo_bar2_id\` int(11) unsigned not null) default character set utf8mb4 engine = InnoDB;');
+    this.addSql('alter table \`test2_bars\` add index \`test2_bars_test2_id_index\`(\`test2_id\`);');
+    this.addSql('alter table \`test2_bars\` add index \`test2_bars_foo_bar2_id_index\`(\`foo_bar2_id\`);');
+    this.addSql('alter table \`test2_bars\` add primary key \`test2_bars_pkey\`(\`test2_id\`, \`foo_bar2_id\`);');
+
     this.addSql('create table \`book2_tags\` (\`order\` int unsigned not null auto_increment primary key, \`book2_uuid_pk\` varchar(36) not null, \`book_tag2_id\` bigint unsigned not null) default character set utf8mb4 engine = InnoDB;');
     this.addSql('alter table \`book2_tags\` add index \`book2_tags_book2_uuid_pk_index\`(\`book2_uuid_pk\`);');
     this.addSql('alter table \`book2_tags\` add index \`book2_tags_book_tag2_id_index\`(\`book_tag2_id\`);');
@@ -150,6 +155,9 @@ export class Migration20191013214813 extends Migration {
     this.addSql('alter table \`publisher2_tests\` add constraint \`publisher2_tests_publisher2_id_foreign\` foreign key (\`publisher2_id\`) references \`publisher2\` (\`id\`) on update cascade on delete cascade;');
     this.addSql('alter table \`publisher2_tests\` add constraint \`publisher2_tests_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;');
 
+    this.addSql('alter table \`test2_bars\` add constraint \`test2_bars_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;');
+    this.addSql('alter table \`test2_bars\` add constraint \`test2_bars_foo_bar2_id_foreign\` foreign key (\`foo_bar2_id\`) references \`foo_bar2\` (\`id\`) on update cascade on delete cascade;');
+
     this.addSql('alter table \`book2_tags\` add constraint \`book2_tags_book2_uuid_pk_foreign\` foreign key (\`book2_uuid_pk\`) references \`book2\` (\`uuid_pk\`) on update cascade on delete cascade;');
     this.addSql('alter table \`book2_tags\` add constraint \`book2_tags_book_tag2_id_foreign\` foreign key (\`book_tag2_id\`) references \`book_tag2\` (\`id\`) on update cascade on delete cascade;');
 
@@ -252,6 +260,11 @@ export class Migration20191013214813 extends Migration {
     "alter table \`publisher2_tests\` add index \`publisher2_tests_publisher2_id_index\`(\`publisher2_id\`);",
     "alter table \`publisher2_tests\` add index \`publisher2_tests_test2_id_index\`(\`test2_id\`);",
     "",
+    "create table \`test2_bars\` (\`test2_id\` int(11) unsigned not null, \`foo_bar2_id\` int(11) unsigned not null) default character set utf8mb4 engine = InnoDB;",
+    "alter table \`test2_bars\` add index \`test2_bars_test2_id_index\`(\`test2_id\`);",
+    "alter table \`test2_bars\` add index \`test2_bars_foo_bar2_id_index\`(\`foo_bar2_id\`);",
+    "alter table \`test2_bars\` add primary key \`test2_bars_pkey\`(\`test2_id\`, \`foo_bar2_id\`);",
+    "",
     "create table \`book2_tags\` (\`order\` int unsigned not null auto_increment primary key, \`book2_uuid_pk\` varchar(36) not null, \`book_tag2_id\` bigint unsigned not null) default character set utf8mb4 engine = InnoDB;",
     "alter table \`book2_tags\` add index \`book2_tags_book2_uuid_pk_index\`(\`book2_uuid_pk\`);",
     "alter table \`book2_tags\` add index \`book2_tags_book_tag2_id_index\`(\`book_tag2_id\`);",
@@ -308,6 +321,9 @@ export class Migration20191013214813 extends Migration {
     "alter table \`publisher2_tests\` add constraint \`publisher2_tests_publisher2_id_foreign\` foreign key (\`publisher2_id\`) references \`publisher2\` (\`id\`) on update cascade on delete cascade;",
     "alter table \`publisher2_tests\` add constraint \`publisher2_tests_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;",
     "",
+    "alter table \`test2_bars\` add constraint \`test2_bars_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;",
+    "alter table \`test2_bars\` add constraint \`test2_bars_foo_bar2_id_foreign\` foreign key (\`foo_bar2_id\`) references \`foo_bar2\` (\`id\`) on update cascade on delete cascade;",
+    "",
     "alter table \`book2_tags\` add constraint \`book2_tags_book2_uuid_pk_foreign\` foreign key (\`book2_uuid_pk\`) references \`book2\` (\`uuid_pk\`) on update cascade on delete cascade;",
     "alter table \`book2_tags\` add constraint \`book2_tags_book_tag2_id_foreign\` foreign key (\`book_tag2_id\`) references \`book_tag2\` (\`id\`) on update cascade on delete cascade;",
     "",
@@ -565,12 +581,27 @@ Array [
   "select 1 (via write connection '127.0.0.1')",
   "release savepointtrx_xx (via write connection '127.0.0.1')",
   "insert into \`mikro_orm_migrations\` (\`name\`) values (?) (via write connection '127.0.0.1')",
+  "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
+  "savepointtrx_xx (via write connection '127.0.0.1')",
+  "select 1 (via write connection '127.0.0.1')",
+  "release savepointtrx_xx (via write connection '127.0.0.1')",
+  "insert into \`mikro_orm_migrations\` (\`name\`) values (?) (via write connection '127.0.0.1')",
   "select table_name as table_name from information_schema.tables where table_type = 'BASE TABLE' and table_schema = schema() (via write connection '127.0.0.1')",
   "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
   "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
+  "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
   "savepointtrx_xx (via write connection '127.0.0.1')",
   "release savepointtrx_xx (via write connection '127.0.0.1')",
   "delete from \`mikro_orm_migrations\` where \`name\` = ? (via write connection '127.0.0.1')",
+  "select table_name as table_name from information_schema.tables where table_type = 'BASE TABLE' and table_schema = schema() (via write connection '127.0.0.1')",
+  "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
+  "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
+  "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
+  "savepointtrx_xx (via write connection '127.0.0.1')",
+  "release savepointtrx_xx (via write connection '127.0.0.1')",
+  "delete from \`mikro_orm_migrations\` where \`name\` = ? (via write connection '127.0.0.1')",
+  "select table_name as table_name from information_schema.tables where table_type = 'BASE TABLE' and table_schema = schema() (via write connection '127.0.0.1')",
+  "select * from \`mikro_orm_migrations\` order by \`id\` asc (via write connection '127.0.0.1')",
   "commit (via write connection '127.0.0.1')",
 ]
 `;
diff --git a/tests/__snapshots__/SchemaGenerator.test.ts.snap b/tests/__snapshots__/SchemaGenerator.test.ts.snap
index 3cbf65f42b12..456359798e64 100644
--- a/tests/__snapshots__/SchemaGenerator.test.ts.snap
+++ b/tests/__snapshots__/SchemaGenerator.test.ts.snap
@@ -74,6 +74,11 @@ create table \`publisher2_tests\` (\`id\` int unsigned not null auto_increment p
 alter table \`publisher2_tests\` add index \`publisher2_tests_publisher2_id_index\`(\`publisher2_id\`);
 alter table \`publisher2_tests\` add index \`publisher2_tests_test2_id_index\`(\`test2_id\`);
 
+create table \`test2_bars\` (\`test2_id\` int(11) unsigned not null, \`foo_bar2_id\` int(11) unsigned not null) default character set utf8mb4 engine = InnoDB;
+alter table \`test2_bars\` add index \`test2_bars_test2_id_index\`(\`test2_id\`);
+alter table \`test2_bars\` add index \`test2_bars_foo_bar2_id_index\`(\`foo_bar2_id\`);
+alter table \`test2_bars\` add primary key \`test2_bars_pkey\`(\`test2_id\`, \`foo_bar2_id\`);
+
 create table \`book2_tags\` (\`order\` int unsigned not null auto_increment primary key, \`book2_uuid_pk\` varchar(36) not null, \`book_tag2_id\` bigint unsigned not null) default character set utf8mb4 engine = InnoDB;
 alter table \`book2_tags\` add index \`book2_tags_book2_uuid_pk_index\`(\`book2_uuid_pk\`);
 alter table \`book2_tags\` add index \`book2_tags_book_tag2_id_index\`(\`book_tag2_id\`);
@@ -130,6 +135,9 @@ alter table \`configuration2\` add constraint \`configuration2_test_id_foreign\`
 alter table \`publisher2_tests\` add constraint \`publisher2_tests_publisher2_id_foreign\` foreign key (\`publisher2_id\`) references \`publisher2\` (\`id\`) on update cascade on delete cascade;
 alter table \`publisher2_tests\` add constraint \`publisher2_tests_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;
 
+alter table \`test2_bars\` add constraint \`test2_bars_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;
+alter table \`test2_bars\` add constraint \`test2_bars_foo_bar2_id_foreign\` foreign key (\`foo_bar2_id\`) references \`foo_bar2\` (\`id\`) on update cascade on delete cascade;
+
 alter table \`book2_tags\` add constraint \`book2_tags_book2_uuid_pk_foreign\` foreign key (\`book2_uuid_pk\`) references \`book2\` (\`uuid_pk\`) on update cascade on delete cascade;
 alter table \`book2_tags\` add constraint \`book2_tags_book_tag2_id_foreign\` foreign key (\`book_tag2_id\`) references \`book_tag2\` (\`id\`) on update cascade on delete cascade;
 
@@ -171,6 +179,7 @@ drop table if exists \`author2_following\`;
 drop table if exists \`author_to_friend\`;
 drop table if exists \`book_to_tag_unordered\`;
 drop table if exists \`book2_tags\`;
+drop table if exists \`test2_bars\`;
 drop table if exists \`publisher2_tests\`;
 drop table if exists \`configuration2\`;
 drop table if exists \`test2\`;
@@ -203,6 +212,7 @@ drop table if exists \`author2_following\`;
 drop table if exists \`author_to_friend\`;
 drop table if exists \`book_to_tag_unordered\`;
 drop table if exists \`book2_tags\`;
+drop table if exists \`test2_bars\`;
 drop table if exists \`publisher2_tests\`;
 drop table if exists \`configuration2\`;
 drop table if exists \`test2\`;
@@ -292,6 +302,11 @@ create table \`publisher2_tests\` (\`id\` int unsigned not null auto_increment p
 alter table \`publisher2_tests\` add index \`publisher2_tests_publisher2_id_index\`(\`publisher2_id\`);
 alter table \`publisher2_tests\` add index \`publisher2_tests_test2_id_index\`(\`test2_id\`);
 
+create table \`test2_bars\` (\`test2_id\` int(11) unsigned not null, \`foo_bar2_id\` int(11) unsigned not null) default character set utf8mb4 engine = InnoDB;
+alter table \`test2_bars\` add index \`test2_bars_test2_id_index\`(\`test2_id\`);
+alter table \`test2_bars\` add index \`test2_bars_foo_bar2_id_index\`(\`foo_bar2_id\`);
+alter table \`test2_bars\` add primary key \`test2_bars_pkey\`(\`test2_id\`, \`foo_bar2_id\`);
+
 create table \`book2_tags\` (\`order\` int unsigned not null auto_increment primary key, \`book2_uuid_pk\` varchar(36) not null, \`book_tag2_id\` bigint unsigned not null) default character set utf8mb4 engine = InnoDB;
 alter table \`book2_tags\` add index \`book2_tags_book2_uuid_pk_index\`(\`book2_uuid_pk\`);
 alter table \`book2_tags\` add index \`book2_tags_book_tag2_id_index\`(\`book_tag2_id\`);
@@ -348,6 +363,9 @@ alter table \`configuration2\` add constraint \`configuration2_test_id_foreign\`
 alter table \`publisher2_tests\` add constraint \`publisher2_tests_publisher2_id_foreign\` foreign key (\`publisher2_id\`) references \`publisher2\` (\`id\`) on update cascade on delete cascade;
 alter table \`publisher2_tests\` add constraint \`publisher2_tests_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;
 
+alter table \`test2_bars\` add constraint \`test2_bars_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;
+alter table \`test2_bars\` add constraint \`test2_bars_foo_bar2_id_foreign\` foreign key (\`foo_bar2_id\`) references \`foo_bar2\` (\`id\`) on update cascade on delete cascade;
+
 alter table \`book2_tags\` add constraint \`book2_tags_book2_uuid_pk_foreign\` foreign key (\`book2_uuid_pk\`) references \`book2\` (\`uuid_pk\`) on update cascade on delete cascade;
 alter table \`book2_tags\` add constraint \`book2_tags_book_tag2_id_foreign\` foreign key (\`book_tag2_id\`) references \`book_tag2\` (\`id\`) on update cascade on delete cascade;
 
@@ -440,6 +458,9 @@ alter table \\"configuration2\\" add constraint \\"configuration2_pkey\\" primar
 
 create table \\"publisher2_tests\\" (\\"id\\" serial primary key, \\"publisher2_id\\" int4 not null, \\"test2_id\\" int4 not null);
 
+create table \\"test2_bars\\" (\\"test2_id\\" int4 not null, \\"foo_bar2_id\\" int4 not null);
+alter table \\"test2_bars\\" add constraint \\"test2_bars_pkey\\" primary key (\\"test2_id\\", \\"foo_bar2_id\\");
+
 create table \\"book2_tags\\" (\\"order\\" serial primary key, \\"book2_uuid_pk\\" varchar(36) not null, \\"book_tag2_id\\" bigint not null);
 
 create table \\"book_to_tag_unordered\\" (\\"book2_uuid_pk\\" varchar(36) not null, \\"book_tag2_id\\" bigint not null);
@@ -472,6 +493,9 @@ alter table \\"configuration2\\" add constraint \\"configuration2_test_id_foreig
 alter table \\"publisher2_tests\\" add constraint \\"publisher2_tests_publisher2_id_foreign\\" foreign key (\\"publisher2_id\\") references \\"publisher2\\" (\\"id\\") on update cascade on delete cascade;
 alter table \\"publisher2_tests\\" add constraint \\"publisher2_tests_test2_id_foreign\\" foreign key (\\"test2_id\\") references \\"test2\\" (\\"id\\") on update cascade on delete cascade;
 
+alter table \\"test2_bars\\" add constraint \\"test2_bars_test2_id_foreign\\" foreign key (\\"test2_id\\") references \\"test2\\" (\\"id\\") on update cascade on delete cascade;
+alter table \\"test2_bars\\" add constraint \\"test2_bars_foo_bar2_id_foreign\\" foreign key (\\"foo_bar2_id\\") references \\"foo_bar2\\" (\\"id\\") on update cascade on delete cascade;
+
 alter table \\"book2_tags\\" add constraint \\"book2_tags_book2_uuid_pk_foreign\\" foreign key (\\"book2_uuid_pk\\") references \\"book2\\" (\\"uuid_pk\\") on update cascade on delete cascade;
 alter table \\"book2_tags\\" add constraint \\"book2_tags_book_tag2_id_foreign\\" foreign key (\\"book_tag2_id\\") references \\"book_tag2\\" (\\"id\\") on update cascade on delete cascade;
 
@@ -500,6 +524,7 @@ drop table if exists \\"author2_following\\" cascade;
 drop table if exists \\"author_to_friend\\" cascade;
 drop table if exists \\"book_to_tag_unordered\\" cascade;
 drop table if exists \\"book2_tags\\" cascade;
+drop table if exists \\"test2_bars\\" cascade;
 drop table if exists \\"publisher2_tests\\" cascade;
 drop table if exists \\"configuration2\\" cascade;
 drop table if exists \\"test2\\" cascade;
@@ -525,6 +550,7 @@ drop table if exists \\"author2_following\\" cascade;
 drop table if exists \\"author_to_friend\\" cascade;
 drop table if exists \\"book_to_tag_unordered\\" cascade;
 drop table if exists \\"book2_tags\\" cascade;
+drop table if exists \\"test2_bars\\" cascade;
 drop table if exists \\"publisher2_tests\\" cascade;
 drop table if exists \\"configuration2\\" cascade;
 drop table if exists \\"test2\\" cascade;
@@ -578,6 +604,9 @@ alter table \\"configuration2\\" add constraint \\"configuration2_pkey\\" primar
 
 create table \\"publisher2_tests\\" (\\"id\\" serial primary key, \\"publisher2_id\\" int4 not null, \\"test2_id\\" int4 not null);
 
+create table \\"test2_bars\\" (\\"test2_id\\" int4 not null, \\"foo_bar2_id\\" int4 not null);
+alter table \\"test2_bars\\" add constraint \\"test2_bars_pkey\\" primary key (\\"test2_id\\", \\"foo_bar2_id\\");
+
 create table \\"book2_tags\\" (\\"order\\" serial primary key, \\"book2_uuid_pk\\" varchar(36) not null, \\"book_tag2_id\\" bigint not null);
 
 create table \\"book_to_tag_unordered\\" (\\"book2_uuid_pk\\" varchar(36) not null, \\"book_tag2_id\\" bigint not null);
@@ -610,6 +639,9 @@ alter table \\"configuration2\\" add constraint \\"configuration2_test_id_foreig
 alter table \\"publisher2_tests\\" add constraint \\"publisher2_tests_publisher2_id_foreign\\" foreign key (\\"publisher2_id\\") references \\"publisher2\\" (\\"id\\") on update cascade on delete cascade;
 alter table \\"publisher2_tests\\" add constraint \\"publisher2_tests_test2_id_foreign\\" foreign key (\\"test2_id\\") references \\"test2\\" (\\"id\\") on update cascade on delete cascade;
 
+alter table \\"test2_bars\\" add constraint \\"test2_bars_test2_id_foreign\\" foreign key (\\"test2_id\\") references \\"test2\\" (\\"id\\") on update cascade on delete cascade;
+alter table \\"test2_bars\\" add constraint \\"test2_bars_foo_bar2_id_foreign\\" foreign key (\\"foo_bar2_id\\") references \\"foo_bar2\\" (\\"id\\") on update cascade on delete cascade;
+
 alter table \\"book2_tags\\" add constraint \\"book2_tags_book2_uuid_pk_foreign\\" foreign key (\\"book2_uuid_pk\\") references \\"book2\\" (\\"uuid_pk\\") on update cascade on delete cascade;
 alter table \\"book2_tags\\" add constraint \\"book2_tags_book_tag2_id_foreign\\" foreign key (\\"book_tag2_id\\") references \\"book_tag2\\" (\\"id\\") on update cascade on delete cascade;
 
@@ -999,6 +1031,11 @@ create table \`publisher2_tests\` (\`id\` int unsigned not null auto_increment p
 alter table \`publisher2_tests\` add index \`publisher2_tests_publisher2_id_index\`(\`publisher2_id\`);
 alter table \`publisher2_tests\` add index \`publisher2_tests_test2_id_index\`(\`test2_id\`);
 
+create table \`test2_bars\` (\`test2_id\` int(11) unsigned not null, \`foo_bar2_id\` int(11) unsigned not null) default character set utf8mb4 engine = InnoDB;
+alter table \`test2_bars\` add index \`test2_bars_test2_id_index\`(\`test2_id\`);
+alter table \`test2_bars\` add index \`test2_bars_foo_bar2_id_index\`(\`foo_bar2_id\`);
+alter table \`test2_bars\` add primary key \`test2_bars_pkey\`(\`test2_id\`, \`foo_bar2_id\`);
+
 create table \`book2_tags\` (\`order\` int unsigned not null auto_increment primary key, \`book2_uuid_pk\` varchar(36) not null, \`book_tag2_id\` bigint unsigned not null) default character set utf8mb4 engine = InnoDB;
 alter table \`book2_tags\` add index \`book2_tags_book2_uuid_pk_index\`(\`book2_uuid_pk\`);
 alter table \`book2_tags\` add index \`book2_tags_book_tag2_id_index\`(\`book_tag2_id\`);
@@ -1055,6 +1092,9 @@ alter table \`configuration2\` add constraint \`configuration2_test_id_foreign\`
 alter table \`publisher2_tests\` add constraint \`publisher2_tests_publisher2_id_foreign\` foreign key (\`publisher2_id\`) references \`publisher2\` (\`id\`) on update cascade on delete cascade;
 alter table \`publisher2_tests\` add constraint \`publisher2_tests_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;
 
+alter table \`test2_bars\` add constraint \`test2_bars_test2_id_foreign\` foreign key (\`test2_id\`) references \`test2\` (\`id\`) on update cascade on delete cascade;
+alter table \`test2_bars\` add constraint \`test2_bars_foo_bar2_id_foreign\` foreign key (\`foo_bar2_id\`) references \`foo_bar2\` (\`id\`) on update cascade on delete cascade;
+
 alter table \`book2_tags\` add constraint \`book2_tags_book2_uuid_pk_foreign\` foreign key (\`book2_uuid_pk\`) references \`book2\` (\`uuid_pk\`) on update cascade on delete cascade;
 alter table \`book2_tags\` add constraint \`book2_tags_book_tag2_id_foreign\` foreign key (\`book_tag2_id\`) references \`book_tag2\` (\`id\`) on update cascade on delete cascade;
 
@@ -1131,6 +1171,9 @@ alter table \\"configuration2\\" add constraint \\"configuration2_pkey\\" primar
 
 create table \\"publisher2_tests\\" (\\"id\\" serial primary key, \\"publisher2_id\\" int4 not null, \\"test2_id\\" int4 not null);
 
+create table \\"test2_bars\\" (\\"test2_id\\" int4 not null, \\"foo_bar2_id\\" int4 not null);
+alter table \\"test2_bars\\" add constraint \\"test2_bars_pkey\\" primary key (\\"test2_id\\", \\"foo_bar2_id\\");
+
 create table \\"book2_tags\\" (\\"order\\" serial primary key, \\"book2_uuid_pk\\" varchar(36) not null, \\"book_tag2_id\\" bigint not null);
 
 create table \\"book_to_tag_unordered\\" (\\"book2_uuid_pk\\" varchar(36) not null, \\"book_tag2_id\\" bigint not null);
@@ -1163,6 +1206,9 @@ alter table \\"configuration2\\" add constraint \\"configuration2_test_id_foreig
 alter table \\"publisher2_tests\\" add constraint \\"publisher2_tests_publisher2_id_foreign\\" foreign key (\\"publisher2_id\\") references \\"publisher2\\" (\\"id\\") on update cascade on delete cascade;
 alter table \\"publisher2_tests\\" add constraint \\"publisher2_tests_test2_id_foreign\\" foreign key (\\"test2_id\\") references \\"test2\\" (\\"id\\") on update cascade on delete cascade;
 
+alter table \\"test2_bars\\" add constraint \\"test2_bars_test2_id_foreign\\" foreign key (\\"test2_id\\") references \\"test2\\" (\\"id\\") on update cascade on delete cascade;
+alter table \\"test2_bars\\" add constraint \\"test2_bars_foo_bar2_id_foreign\\" foreign key (\\"foo_bar2_id\\") references \\"foo_bar2\\" (\\"id\\") on update cascade on delete cascade;
+
 alter table \\"book2_tags\\" add constraint \\"book2_tags_book2_uuid_pk_foreign\\" foreign key (\\"book2_uuid_pk\\") references \\"book2\\" (\\"uuid_pk\\") on update cascade on delete cascade;
 alter table \\"book2_tags\\" add constraint \\"book2_tags_book_tag2_id_foreign\\" foreign key (\\"book_tag2_id\\") references \\"book_tag2\\" (\\"id\\") on update cascade on delete cascade;
 
diff --git a/tests/entities-sql/FooBar2.ts b/tests/entities-sql/FooBar2.ts
index d492ee27f03e..8f33d738ac7d 100644
--- a/tests/entities-sql/FooBar2.ts
+++ b/tests/entities-sql/FooBar2.ts
@@ -1,6 +1,7 @@
-import { ArrayType, BlobType, Entity, Formula, JsonType, OneToOne, PrimaryKey, Property } from '@mikro-orm/core';
+import { ManyToMany, Collection, Entity, Formula, JsonType, OneToOne, PrimaryKey, Property } from '@mikro-orm/core';
 import { BaseEntity22 } from './BaseEntity22';
 import { FooBaz2 } from './FooBaz2';
+import { Test2 } from './Test2';
 
 @Entity()
 export class FooBar2 extends BaseEntity22 {
@@ -32,6 +33,9 @@ export class FooBar2 extends BaseEntity22 {
   @Formula(`(select 123)`)
   random?: number;
 
+  @ManyToMany(() => Test2, t => t.bars)
+  tests = new Collection<Test2>(this);
+
   static create(name: string) {
     const bar = new FooBar2();
     bar.name = name;
diff --git a/tests/entities-sql/Test2.ts b/tests/entities-sql/Test2.ts
index b0164719cfd7..bfde357b0b9c 100644
--- a/tests/entities-sql/Test2.ts
+++ b/tests/entities-sql/Test2.ts
@@ -1,6 +1,7 @@
-import { Collection, Entity, OneToMany, OneToOne, PrimaryKey, Property } from '@mikro-orm/core';
+import { Collection, Entity, ManyToMany, OneToMany, OneToOne, PrimaryKey, Property } from '@mikro-orm/core';
 import { Book2 } from './Book2';
 import { Configuration2 } from './Configuration2';
+import { FooBar2 } from './FooBar2';
 
 @Entity()
 export class Test2 {
@@ -20,6 +21,9 @@ export class Test2 {
   @Property({ version: true })
   version!: number;
 
+  @ManyToMany(() => FooBar2)
+  bars = new Collection<FooBar2>(this);
+
   constructor(props: Partial<Test2> = {}) {
     this.id = props.id!;
     this.name = props.name!;
diff --git a/tests/issues/GH369.test.ts b/tests/issues/GH369.test.ts
index 717da7620a5f..3f28bb68a5b1 100644
--- a/tests/issues/GH369.test.ts
+++ b/tests/issues/GH369.test.ts
@@ -34,10 +34,9 @@ describe('GH issue 369', () => {
   beforeAll(async () => {
     orm = await MikroORM.init({
       entities: [A, B],
-      dbName: __dirname + '/../../temp/mikro_orm_test_gh369.db',
+      dbName: ':memory:',
       type: 'sqlite',
     });
-    await new SchemaGenerator(orm.em).dropSchema();
     await new SchemaGenerator(orm.em).createSchema();
   });
 
diff --git a/tests/issues/GH467.test.ts b/tests/issues/GH467.test.ts
index 54f5febcbc28..8219cf778a47 100644
--- a/tests/issues/GH467.test.ts
+++ b/tests/issues/GH467.test.ts
@@ -30,10 +30,9 @@ describe('GH issue 467', () => {
   beforeAll(async () => {
     orm = await MikroORM.init({
       entities: [A, B],
-      dbName: __dirname + '/../../temp/mikro_orm_test_gh467.db',
+      dbName: ':memory:',
       type: 'sqlite',
     });
-    await orm.getSchemaGenerator().dropSchema();
     await orm.getSchemaGenerator().createSchema();
   });
 
diff --git a/tests/mysql-schema.sql b/tests/mysql-schema.sql
index 27f6ae5a3824..59c4e1bfceb7 100644
--- a/tests/mysql-schema.sql
+++ b/tests/mysql-schema.sql
@@ -7,6 +7,7 @@ drop table if exists `author_to_friend`;
 drop table if exists `book_to_tag_unordered`;
 drop table if exists `book2_tags`;
 drop table if exists `publisher2_tests`;
+drop table if exists `test2_bars`;
 drop table if exists `configuration2`;
 drop table if exists `test2`;
 drop table if exists `book2`;
@@ -115,6 +116,11 @@ create table `publisher2_tests` (`id` int unsigned not null auto_increment prima
 alter table `publisher2_tests` add index `publisher2_tests_publisher2_id_index`(`publisher2_id`);
 alter table `publisher2_tests` add index `publisher2_tests_test2_id_index`(`test2_id`);
 
+create table `test2_bars` (`test2_id` int(11) unsigned not null, `foo_bar2_id` int(11) unsigned not null) default character set utf8mb4 engine = InnoDB;
+alter table `test2_bars` add index `test2_bars_test2_id_index`(`test2_id`);
+alter table `test2_bars` add index `test2_bars_foo_bar2_id_index`(`foo_bar2_id`);
+alter table `test2_bars` add primary key `test2_bars_pkey`(`test2_id`, `foo_bar2_id`);
+
 create table `book2_tags` (`order` int unsigned not null auto_increment primary key, `book2_uuid_pk` varchar(36) not null, `book_tag2_id` bigint unsigned not null) default character set utf8mb4 engine = InnoDB;
 alter table `book2_tags` add index `book2_tags_book2_uuid_pk_index`(`book2_uuid_pk`);
 alter table `book2_tags` add index `book2_tags_book_tag2_id_index`(`book_tag2_id`);
@@ -172,6 +178,9 @@ alter table `configuration2` add constraint `configuration2_test_id_foreign` for
 alter table `publisher2_tests` add constraint `publisher2_tests_publisher2_id_foreign` foreign key (`publisher2_id`) references `publisher2` (`id`) on update cascade on delete cascade;
 alter table `publisher2_tests` add constraint `publisher2_tests_test2_id_foreign` foreign key (`test2_id`) references `test2` (`id`) on update cascade on delete cascade;
 
+alter table `test2_bars` add constraint `test2_bars_test2_id_foreign` foreign key (`test2_id`) references `test2` (`id`) on update cascade on delete cascade;
+alter table `test2_bars` add constraint `test2_bars_foo_bar2_id_foreign` foreign key (`foo_bar2_id`) references `foo_bar2` (`id`) on update cascade on delete cascade;
+
 alter table `book2_tags` add constraint `book2_tags_book2_uuid_pk_foreign` foreign key (`book2_uuid_pk`) references `book2` (`uuid_pk`) on update cascade on delete cascade;
 alter table `book2_tags` add constraint `book2_tags_book_tag2_id_foreign` foreign key (`book_tag2_id`) references `book_tag2` (`id`) on update cascade on delete cascade;
 
diff --git a/tests/postgre-schema.sql b/tests/postgre-schema.sql
index b6edaf1e360d..d5f642a5c17d 100644
--- a/tests/postgre-schema.sql
+++ b/tests/postgre-schema.sql
@@ -6,6 +6,7 @@ drop table if exists "author_to_friend" cascade;
 drop table if exists "book_to_tag_unordered" cascade;
 drop table if exists "book2_tags" cascade;
 drop table if exists "publisher2_tests" cascade;
+drop table if exists "test2_bars" cascade;
 drop table if exists "configuration2" cascade;
 drop table if exists "test2" cascade;
 drop table if exists "book2" cascade;
@@ -66,6 +67,9 @@ alter table "configuration2" add constraint "configuration2_pkey" primary key ("
 
 create table "publisher2_tests" ("id" serial primary key, "publisher2_id" int4 not null, "test2_id" int4 not null);
 
+create table "test2_bars" ("test2_id" int4 not null, "foo_bar2_id" int4 not null);
+alter table "test2_bars" add constraint "test2_bars_pkey" primary key ("test2_id", "foo_bar2_id");
+
 create table "book2_tags" ("order" serial primary key, "book2_uuid_pk" varchar(36) not null, "book_tag2_id" bigint not null);
 
 create table "book_to_tag_unordered" ("book2_uuid_pk" varchar(36) not null, "book_tag2_id" bigint not null);
@@ -98,6 +102,9 @@ alter table "configuration2" add constraint "configuration2_test_id_foreign" for
 alter table "publisher2_tests" add constraint "publisher2_tests_publisher2_id_foreign" foreign key ("publisher2_id") references "publisher2" ("id") on update cascade on delete cascade;
 alter table "publisher2_tests" add constraint "publisher2_tests_test2_id_foreign" foreign key ("test2_id") references "test2" ("id") on update cascade on delete cascade;
 
+alter table "test2_bars" add constraint "test2_bars_test2_id_foreign" foreign key ("test2_id") references "test2" ("id") on update cascade on delete cascade;
+alter table "test2_bars" add constraint "test2_bars_foo_bar2_id_foreign" foreign key ("foo_bar2_id") references "foo_bar2" ("id") on update cascade on delete cascade;
+
 alter table "book2_tags" add constraint "book2_tags_book2_uuid_pk_foreign" foreign key ("book2_uuid_pk") references "book2" ("uuid_pk") on update cascade on delete cascade;
 alter table "book2_tags" add constraint "book2_tags_book_tag2_id_foreign" foreign key ("book_tag2_id") references "book_tag2" ("id") on update cascade on delete cascade;
 
diff --git a/yarn.lock b/yarn.lock
index 899906ef8eb7..933e3303bd47 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -3502,10 +3502,10 @@ escape-string-regexp@^2.0.0:
   resolved "https://registry.yarnpkg.com/escape-string-regexp/-/escape-string-regexp-2.0.0.tgz#a30304e99daa32e23b2fd20f51babd07cffca344"
   integrity sha512-UpzcLCXolUWcNu5HtVMHYdXJjArjsF9C0aNnquZYY4uW/Vu0miy5YoWvbV345HauVvcAUnpRuhMMcqTcGOY2+w==
 
-escaya@^0.0.47:
-  version "0.0.47"
-  resolved "https://registry.yarnpkg.com/escaya/-/escaya-0.0.47.tgz#4316a68fe4f7ee43681a72de17f2d4b2adcfd4ff"
-  integrity sha512-dVhBDCcUY5Rva78u3SqGxBOihUGsz4JI4l0pta8GiN5tRLMucshTZ6ntq3FPw1LBuRbjcObb45INPwYxiqEvvQ==
+escaya@^0.0.49:
+  version "0.0.49"
+  resolved "https://registry.yarnpkg.com/escaya/-/escaya-0.0.49.tgz#3295f5c3a1cb2c29cf8cd839fbf4240cc422f278"
+  integrity sha512-Wo5yFmYe+8+YSDztQzJ4LplPttNmQl4rb3TjyAR6zvZUgWiPKjacXLGvdtqprHCK+Z1mVWcAKACRKlYF9JgqDg==
 
 escodegen@^1.14.1:
   version "1.14.3"
@@ -4536,7 +4536,7 @@ iconv-lite@0.4.24, iconv-lite@^0.4.24, iconv-lite@^0.4.4:
   dependencies:
     safer-buffer ">= 2.1.2 < 3"
 
-iconv-lite@^0.5.0, iconv-lite@^0.5.1:
+iconv-lite@^0.5.1:
   version "0.5.2"
   resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.5.2.tgz#af6d628dccfb463b7364d97f715e4b74b8c8c2b8"
   integrity sha512-kERHXvpSaB4aU3eANwidg79K8FlrN77m8G9V+0vOR3HYaRifrlwMEpT7ZBJqLSEIHnEgJTHcWK82wwLwwKwtag==
@@ -5907,6 +5907,13 @@ lru-cache@^5.1.1:
   dependencies:
     yallist "^3.0.2"
 
+lru-cache@^6.0.0:
+  version "6.0.0"
+  resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-6.0.0.tgz#6d6fe6570ebd96aaf90fcad1dafa3b2566db3a94"
+  integrity sha512-Jo6dJ04CmSjuznwJSS3pUeWmd/H0ffTlkXXgwZi+eq1UCmqQwCh+eLsYOYCwY991i2Fah4h1BEMCx4qThGbsiA==
+  dependencies:
+    yallist "^4.0.0"
+
 macos-release@^2.2.0:
   version "2.4.1"
   resolved "https://registry.yarnpkg.com/macos-release/-/macos-release-2.4.1.tgz#64033d0ec6a5e6375155a74b1a1eba8e509820ac"
@@ -6346,15 +6353,16 @@ mute-stream@~0.0.4:
   resolved "https://registry.yarnpkg.com/mute-stream/-/mute-stream-0.0.8.tgz#1630c42b2251ff81e2a283de96a5497ea92e5e0d"
   integrity sha512-nnbWWOkoWyUsTjKrhgD0dcz22mdkSnpYqbEjIm2nhwhuxlSkpywJmBo8h0ZqJdkp73mb90SssHkN4rsRaBAfAA==
 
-mysql2@sidorares/node-mysql2#master:
-  version "2.1.0"
-  resolved "https://codeload.github.com/sidorares/node-mysql2/tar.gz/3133dc12e969c650f2e6a586e17af26f268599f0"
+mysql2@^2.2.5:
+  version "2.2.5"
+  resolved "https://registry.yarnpkg.com/mysql2/-/mysql2-2.2.5.tgz#72624ffb4816f80f96b9c97fedd8c00935f9f340"
+  integrity sha512-XRqPNxcZTpmFdXbJqb+/CtYVLCx14x1RTeNMD4954L331APu75IC74GDqnZMEt1kwaXy6TySo55rF2F3YJS78g==
   dependencies:
     denque "^1.4.1"
     generate-function "^2.3.1"
-    iconv-lite "^0.5.0"
+    iconv-lite "^0.6.2"
     long "^4.0.0"
-    lru-cache "^5.1.1"
+    lru-cache "^6.0.0"
     named-placeholders "^1.1.2"
     seq-queue "^0.0.5"
     sqlstring "^2.3.2"
@@ -9253,6 +9261,11 @@ yallist@^3.0.0, yallist@^3.0.2, yallist@^3.0.3:
   resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.1.1.tgz#dbb7daf9bfd8bac9ab45ebf602b8cbad0d5d08fd"
   integrity sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==
 
+yallist@^4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/yallist/-/yallist-4.0.0.tgz#9bb92790d9c0effec63be73519e11a35019a3a72"
+  integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==
+
 yaml@^1.10.0, yaml@^1.7.2:
   version "1.10.0"
   resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.0.tgz#3b593add944876077d4d683fee01081bd9fff31e"