Stages in Knuckles' Chaotix are referred to as Attractions. Much like Sonic CD, attractions are named with Both words starting with the same letter, and aren't followed by "Zone" as is the custom in 2D Sonic games. Each area has 5 levels, and the 5th culminates in a boss battle.
- Isolated Island/Practice Stage: A special isolated area played before the main game to get players acquainted with the special unique maneuvers introduced into the game. There are no enemies here, and it features many of the new item boxes, such as Large Size and Small size boxes. Not much happens here.
- Botanic Base: The island's most natural attraction is this giant greenhouse, filled with oddly geometric trees, and a jungle of hostile flora. the first level is VERY short.
- Speed Slider: A roller coaster reminiscent of Casino Night and Carnival Night Zone, Speed Slider is the fastest attraction in Knuckles' Chaotix. The level moves all the way to a confrontation with Dr. Eggman on his carousel. Speed Slider resembles a stage in the prototype Sonic Crackers.
- Amazing Arena: At the start of this stage, the player is in the dark, but once the light switch is hit, Amazing Arena turns bright and colorful. If the player fails to locate it, the stage starts all over again. There are also platforms that float to specific points on the opposite sides of the level and tubes that suck the player into them, much like in Chemical Plant Zone of Sonic the Hedgehog 2. This is probably one of the most frustrating stages.
- Techno Tower: A futuristic-styled tower that the player must climb. In Level 5, the player can hop on a drill machine that burrows through solid walls. There are Eggman images all over, and they can be entered, often concealing hidden item boxes.
- Marina Madness: A cruise-themed attraction with, curiously, no water. The player must jump from ship to ship to complete this level while dodging flying fish and sailing stingrays. the Ships move up and down with the waves, which can sometimes make navigating difficult.
- World Entrance: Between each stage the player visits the World Entrance. Here, one can choose to end the game, select a new partner, and choose a new stage. New partners are chosen with the "Combi-catcher", a semi-random chooser. Levels are picked the same way, by bashing a sphere and stopping the levels from being lit up.