The game, similar to its predecessor Super Nazo Puyo: Rulue no Roux focuses on puzzle solving using standard Puyo Puyo gameplay. The player is tasked with varies clearing objectives using preset boards and pieces, ranging from clearing all of a specific color of Puyo, clearing all Nuisance Puyo, creating a specific chain length, clearing a certain amount of Puyo simultaneously, or simply clearing the whole board. Every time the player fails to complete a puzzle their health will decrease, as indicated by Rulue's expressions and the Puyo above her head slowly dipping below the bar. If the player loses all their health, the player will receive a Game Over and can choose to restart from the last character talked to or quit back to the title screen. Gauges on the right side of the screen will fill up with each completed puzzle and, once completely filled, will completely restore the player's health. The player can also climb and double rotate, and how many puzzles that need to be complete within each set is indicated by stars that fill up with each completed puzzle.
Unlike its predecessor, the game adopts a RPG style with an overworld, NPCs, and items. As the player progresses through the game they have to complete quests in the overworld by retrieving items or talking to NPCs, exploring 6 major locations doing so; this causes the game to be less linear then its predecessor. The game is also saved in the menu, while its predecessor saves automatically.
