During the development of Harry Potter and the Sorcerer's Stone, and Harry Potter and the Chamber of Secrets, EA forbade the developers from including Harry Potter characters that only appeared in the books and not the movies, as Warner Bros. enforced strict policies in an attempt to keep unauthorized on-set footage or photos from leaking. EA was more focused on the home console and Game Boy Advance versions and, as such, they paid very little attention to the Game Boy Color version; EA would be impressed regardless that the developers created a game for a less powerful console than the next-generation ones. Because of this, the Game Boy Color versions of both games were a more faithful adaptation of the original two books. Ironically, Peeves, despite being cut from the first Harry Potter film, appears in the games anyway because Warner Bros. didn't tell EA that he was cut from the movie until the last month of development.

The development teams of the different versions actually shared concept art between them during the planning stages of development. After that, the developers were on their own as they thought the different versions would appeal to different audiences. For instance, The PC devs designed their game to be more appealing toward children and pre-teens.

Despite being developed by different studios, in all versions but the Game Boy Color version, during the final battle with Voldemort Spoiler:/Professor Quirrell, the player must use the Mirror of Erised in the middle of the room in order to strike and defeat him. This does not happen in either the book or movie version of the story. Spoiler:In those stories, Harry involuntarily "defeats" Lord Voldemort when the villain tries to touch him only for Lily Potter's protection spell that she put on Harry to disintegrate Quirrell and in turn Voldemort's physical vessel.