The gameplay involves randomly generated dungeons and turn-based battles of the Chocobo's Mystery Dungeon title, though new elements have also been incorporated into the gameplay, such as the Job system featuring ten jobs.[10][11] Different jobs change the appearance of the player's Chocobo and alter the layout of the dungeons the players enter.[11] "Pop-up duels" also make a comeback with the addition of enemy cards that can be brought to "Mog's House", where they can be used to play minigames such as "bat shooter", "kick darts", fishing, and gardening.[11]
The player uses the Wii Remote to control characters. The player can also choose to use the Classic Controller if preferred.[12] As the player moves, Chocobo regains health, and if the player loses all of his or her health, he or she will be brought back to the beginning of the current dungeon.[13] The game is Wi-Fi compatible, and players can battle against other players.[11]