In the SNES version, enemy changes and Autumn-colored levels appear after completing the Special World. In the Game Boy Advance version, all 96 exits must be cleared instead.

Additionally, the Game Boy Advance version includes a cutscene showing Luigi in a balloon tossing out masks to the Koopas after unlocking the Autumn-colored levels, whereas the changes in the SNES version are first seen when entering Yoshi's house upon exiting the Special World.

Galoombas and Pokeys also have different appearances in the Game Boy Advance version, along with Koopas, Bullet Bills and Piranha plants like the SNES version.