Mini-Games can only be played in single or multiplayer Adventure Mode. There are two optional Mini-Games to play from, and one of each mini-game can be found in the hub world of each Zone. The entrance to a Mini-Game is a blue, dome shaped transporter with a Bumper-styled symbol in its center. To play a Mini-Game, one must locate a transporter within the Zone map. There is no difference between the domes of both Mini-Games. Once a Mini-Game has been played, the dome transporter darkens, and the Mini-Game for that Zone can no longer be played for the remainder of the adventure session (the Mini-gGames can be replayed if system is reset).
Players have a set amount of time to complete a mini-game. The two different styles of Mini-Games are as follows:
- Defeat all Enemies: Players have to defeat all eight enemies scattered throughout the layout of this Mini-Game. Characters do not die while taking damage from an enemy, and no Rings can be found. The gimmicks and enemies are all based off of the current Zone that the player enters from. These Mini-Games start with a one minute time limit.
- Push the Switch and get (x) Points: There is a giant Capsule with five switches in the center of the stage (one switch on top and two on each of its sides). To obtain points, the player must hit the switches when they are glowing, and obtain the required amount of points within 30 seconds. Only one switch may glow at a time, and will glow randomly on any of its five positions (it may also repeat a glow on the switch it was just on). The glowing switch starts off as a red color, but will quickly change to yellow, then blue. The color signifies the amount of points a player will receive:
- Red = 3 points
- Yellow = 2 points
- Blue = 1 point
- Each Zone map will also have a different amount of points to accumulate, with a higher number Zone having a higher requirement.
To obtain extra lives from these minigames, the time requirements from the Mini-Game being played must be fulfilled upon clearing. The amount of lives received vary on the time completion requirements:
- 16 or more seconds remaining = x5 extra lives
- Between 6 seconds and 14 seconds, 99 milliseconds remaining = x2 extra lives
- Below 6 seconds remaining = x1 extra life
- In the Defeat all Enemies Mini-Game, no Rings are dropped from enemies. Instead, a flower seed emerges. This is similar what happens with the enemies in Sonic the Hedgehog CD.
- The Defeat all Enemies Mini-Game in Zone 5 is the only Mini-Game the player may fail in without getting a Time Up.