Mother 3's Main Theme "Love Theme" wasn't created until far into the game's development. Itoi said that it didn't even exist in December 2005, a mere 4 months before the game's release.

The "Ok desu ka" that sounds on the Character Naming screen is voiced by Shigesato Itoi, who was tricked into saying it into a hidden tape recorder by Hirokazu Tanaka, the music composer for the Mother 1 and Mother 2.

In Chapter 7, when a hooded Mr. Saturn gives you back the Courage Badge, he says goodbye to the player and walks a few spaces offscreen where it is supposed to stop and disappear. However, due to a bug, he remains in that spot, just a few spaces away from the player. Itoi liked this bug, so he decided to keep it there and write some text for him.

An interview by creator Shigesato Itoi reveals that if Claus managed to pull the final needle Spoiler:to awaken the dragon, then all of existence would have been erased, including the dragon itself.

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.