Waku-waku Puyo Puyo Dungeon is a roguelike dungeon crawler featuring characters from the Madou Monogatari and Puyo Puyo franchises.

A high-tech amusement park known as Waku Waku Puyo Puyo Land, known for its ever-changing mazes, is awarding people who successfully clear the park attractions a "Great Magic Item." Arle hears of it one day upon encountering Doppelganger Schezo on a walk, and decides to investigate on what it is. Rulue enthusiastically pursues the prize, seeing it as her chance to finally obtain magic. Schezo, lastly, visits the amusement park in order to restore his lost magic power.