Editing Minigame

*In the Leg Outpost, when Bowser performs tasks that involve pushing objects using his legs, Mario and Luigi visit this area to play a minigame which requires them stomping on Bowser's leg muscles to make him move faster. The player must press the correct, corresponding brother button to make Mario and Luigi press down on the muscle when they land, making Bowser push the object forward. After stomping down on each muscle a set number of times, Mario and Luigi will separate, and the player must press both brother buttons to press down on both muscles, causing Bowser to push even further forward. This area is visited two times throughout the course of the game.

*In the Nose Deck, when Bowser smells certain aroma, Mario and Luigi have to go to this area due to an odd disturbance. The minigame starts once the brothers enter a cyclone. Like with the carrot minigame, the player utilizes the stylus to launch the [[Spin Jump (Mario & Luigi series)|spinning]] brothers into pollen so they knock it into ten large nasal mounds on the side, turning them from blue to pink. Once enough pollen is knocked, a large mound will appear, which the brothers must spin into. Spiked pollen will start to appear after this is done, which will take away a heart from the player when they are touched, so they must be avoided while hitting the large mounds that sporadically appear from time to time. After enough mounds are hit, the minigame is over and Bowser will let out a large sneeze, which is required at certain points in the game to progress. This area is revisited three times.

*In the Chest Station, when Bowser is burned while he is curled up into a ball, Mario and Luigi visit this area. The minigame starts once the brothers enters a cannon in the area, sending them into a small area as a ball, which requires the player to use the stylus to bring back the brothers and fling them in a direction, causing Bowser to boost upwards in that same direction. If Bowser gets hit, he loses a few coins or a hit point, depending on the current minigame being  played. This area is visited twice, the first time the brothers visit this area is when two giant [[Fire Piranha Plant|fire-breathing]] [[Piranha Plant]]s burn Bowser as he is storming [[Peach's Castle#Mario & Luigi: Bowser's Inside Story / Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey|Peach's Castle]], and a second time when Bowser meets up with (the now-completed) [[Dark Bowser]] deeper into the castle and battles him with the [[spike ball (move)|spike ball]] technique.

Besides those minigames, the player can play the [[Cholesteroad]] minigame in the [[Challenge Node]], where they are tested into using their acquired [[Bros. Attack|Special Attacks]] to defeat [[Cholesteron]]s and earn enough points to win prizes. There are also minigames that are played outside of Bowser's body, like [[Broque Madame]]'s minigame in [[Blubble Lake]], where the player is tested into using their acquired [[Brawl Attack]]s to earn points and win points, similar to the Cholesteroad.