The SNES version of the game has the same form of VS mode and Action mode as its predecessor. However, there are some notable differences available between the old and new versions. First, the graphics are vastly improved, and infused with rich colors that make the game much more aesthetically pleasing than the early versions of the game. The design for Yoshi is another important difference, evolving from his NES incarnation into one that is more similar to the one seen in Yoshi's Island.

The SNES version has an additional puzzle mode where players have to clear the game board in a limited number of moves. There are 100 unique puzzles in this mode.