Production of the movie became too time consuming, and with the deadline for the completed project fast approaching, several scenes in the original script had to be re-written to make them simpler for the animators to animate (including the sacrificing scene), or cut from the script completely, thus resulting in a much shorter movie with fewer locations The Chipmunks and Chipettes actually visit.
At various points in the film, Miss Miller sings "Come On-a My House" and "Witch Doctor". Both songs were written by Ross Bagdasarian, creator of the Chipmunks and father to the film's writer/producer/star Ross Bagdasarian Jr..
Bagdasarian Productions hired former Disney animators Dan Haskett, Glen Keane, and David Pruiksma to work on this film after they had been laid off by Disney following the box office failure of The Black Cauldron (1985). Disney eventually re-hired the animators.
Ross Bagdasarian Jr. and Janice Karman were married during production of this movie, and are still married as of 2025. Bagdasarian co-wrote the story and screenplay, produced the film, and provided the voices of Alvin, Simon, and David Seville. Karman directed the film, co-wrote the story and screenplay, and provided the voices of Theodore and all three Chipettes. Bagdasarian and Karman also remain co-directors of Bagdasarian Productions.
The original release date was intended to be around Christmas 1986. Production delays prompted the film's release to be pushed to May of the following year.