Mother 3 was originally going to be a 3D game for the Nintendo 64 DD add-on. Dubbed "Earthbound 64" by fans, the game was delayed several times due to the little experience the development team had with 3D games. The game would have possibly utilized the N64 DD's features and would also possibly use Mario Artist to create new in-game character faces. The Rumble Pak was also considered to be used during battle sequences. Due to the commercial failure of the N64 DD, the game was canceled but later recreated for the Game Boy Advance.

During development of EarthBound 64, Shigesato Itoi thought about making a Mr. Saturn spin-off action puzzle game, but this never materialized.

Footage of the game taken during its development period on the Nintendo 64DD shows Ness, the protagonist from EarthBound, to be a playable character. The footage shows Ness riding the Pork Bean through a desert area, as well as him running through a jungle.

Mother 3+, the game's physical soundtrack, contains a remix of Big Shot's theme. This remix is heavily based on the theme used in the trailer for Earthbound/Mother 64. The track's name, "A Great Person Theme", instead of "Big Shot's Theme", suggests that this particular version of the song was created earlier in the game's development, possibly when it was still planned to be a 64DD game.