Production ended November 2018, and the film was initially scheduled for release at the Cannes Film Festival in 2019, but in December 2018, director Paul Verhoeven had to undergo surgery for a hip injury suffered due to the set's location, which involved lots of hills and climbing. Post-production in Amsterdam had to be delayed until June 2019 to allow time for him to recover from his surgery. However, subsequent complications from pain medication caused an intestinal obstruction that ended in a life-threatening colon perforation; fortunately, Verhoeven's wife urged him to go to the hospital in time. Verhoeven and producer Saïd Ben Saïd agreed to delay the release to 2020 in order for Verhoeven to recover, and be fully present during the post-production process. Verhoeven still credits his editor Job ter Burg for finishing much of the film on his own while he himself was recovering and unable to attend. Eventually, the world-wide COVID-19 pandemic caused the movie to be delayed for another year.
At the Cannes Film Festival press conference, Paul Verhoeven was upset at the suggestion that his film is in any way blasphemous. "I do not understand really how you can be blasphemous about something that happened. You cannot basically change history after the fact. You can talk about that was wrong or not, but you cannot change history. I think the word blasphemy for me in this case is stupid." Some critics pointed out he may not understand the definition of "blasphemous" based on his response.
When Judith C. Brown's book 'Immodest Acts' came out in 1987, screenwriter Gerard Soeteman was immediately intrigued, and brought the book to his long-time collaborator, director Paul Verhoeven, with the idea to turn it into a movie. Soeteman wrote an early treatment, but due to script problems and Verhoeven's American career taking flight, the project was shelved. Decades later, producer Saïd Ben Saïd finally picked the film up for production based on the original outline, and Soeteman then wrote two versions of the script. However, he wasn't involved in later re-writes by David Birke and director Paul Verhoeven, and declined any credit, citing his dissatisfaction with the movie's emphasis on sexual content. Soeteman wanted the movie to be about a woman's struggle for power through religion in a male-dominated world, but was reportedly disappointed that Verhoeven had ditched many of those feminist elements in his script in favor of "fumbling with genitals." Verhoeven defended himself by stating that the source novel had the second title 'The Life of a Lesbian Nun in Renaissance Italy' for a reason, and he felt that depicting the sexual side of Benedetta's life explicitly and without prudish restraints was vital to the subject matter. He also believed that Benedetta's motivation for becoming abbess was not to attain power, but simply because it afforded her a private room, so she could consummate her relationship with Bartolomea in secret.
The movie features plenty of sex and nudity, but director Paul Verhoeven stated that the actors themselves served as 'intimacy coordinators'; everything was discussed and storyboarded beforehand, so that there were no surprises on set. Verhoeven even asked main star Virginie Efira not to read the book, he simply warned her about the sex scenes, to which she had no objections. All the actors concurred in interviews that they were unfazed. Efira believes, "Sexuality is an interesting subject. There aren't that many directors who know how to film it. Paul has known from the beginning and is someone who has dealt with this major topic in an amazing way. Nudity is of no interest when it's not depicted in a beautiful way, that's not what Paul does. Everything was very joyful when we stripped off our clothes." Daphné Patakia, who plays Sister Bartolomea, concurred, "You forget there are these naked bodies. I have the impression that even in Paul's other films, these scenes where people are nude or making love, well they speak reams." Verhoeven said that he had chosen Patakia because of the lightness and humor she had displayed during her audition, which was exactly what he wanted to keep the sex scenes from becoming heavy. Patakia in turn didn't hesitate for a second when she was approached for the role; even though there are love scenes which might have been "a bit scary, [Verhoeven] immediately talked to me about the love scenes so I knew exactly how they were going to be shot." Verhoeven chimed in, "In general, when people have sex, they take their clothes off so I'm stunned by the fact that we don't want to look at the reality of life. Why this puritanism has been introduced is, in my opinion, wrong."
According to Paul Verhoeven, he received threatening letters from religious groups when the movie was announced, and the Catholic League even tried to stop its release. They protested mostly against the original title, 'Blessed Virgin', as they initially believed it was about the Virgin Maria; when corrected, they argued that the title Blessed Virgin should only be used for Maria, so the film's title was changed to 'Benedetta'. The Catholics were also outraged about the original poster, which showed a nun with one breast exposed, so a more modest poster with the cast's faces was made for the American market (although Verhoeven noted that most European countries still preferred the nude poster). The film's North American premiere at the New York Film Festival was protested by members of The American Society for the Defense of Tradition, Family and Property. The protesters were accompanied with bagpipes and signs that said, "Why the endless insults to Jesus?" and "We vehemently protest the blasphemous lesbian movie Benedetta that insults the sanctity of Catholic nuns." In Russia, the movie was banned completely because of its perceived blasphemic content and promotion of homosexuality.