Super Bust-A-Move introduces some new elements to the series (and removes some others): Large bubbles are found in certain levels. Shooting a bubble of the same color at them makes every bubble in the level change into that color. In some levels, the pointer and the bubbles that are shot are of a very small size, enabling the player to shoot bubbles between small gaps. These bubbles grow into normal size after being clustered. Occasionally, a conveyor belt will surround the level. This makes bouncing off the ceiling and the walls significantly tricky, since the bubbles' trajectory will change upon bouncing. Levels do not always have the usual rectangular shape. Some of them are jagged or have walls inside them, which forces the player to change strategy. Small blocks appear in some levels. They change the bubbles' trajectories, much like walls, but they move down with the level and fall off when they touch the line. The pulley system introduced in Puzzle Bobble 4 is nowhere to be seen. Chain Reaction is only present in 2P battles, but it is completely optional.

The gameplay is standard Puzzle Bobble action, but with features brought over from the arcade iteration of Super Puzzle Bobble such as giant and mini bubbles (with the sole exception being co-op. ) The GameCube ports outside North America are a later version of the game and includes bonus game modes called "Shoot Bubble" that plays in a similar fashion to Space Invaders and "4P Battle" where up to four players complete their puzzle first before the others.