Minna de Puyo Puyo

The game is divided into several modes. The Single Puyo Puyo mode is essentially the game's story mode. Each course is unlocked as Arle Nadja progresses through the story. An interesting feature of this mode is the ability to attain and deliver various items throughout the courses.

The item side quest can be played after clearing the game. Each item is received after the player completes the course for the second time. The player navigates through six different areas - Hamaji Forest, Gold Town, Gachinko Dungeon, Magical Tower, Dark Prince Castle and Trial Labyrinth - each with their own Special Rule. The first five areas are each unlocked by completing the one before it, but Trial Labyrinth has to be unlocked after completing an item delivery quest following the completion of the first five areas a second time.

Double Puyo Puyo and Everybody Puyo Puyo are the game's two player and four player modes respectively. They allow for both single and multi-cart play. The Point and Hard Puyo rules can be used once they are unlocked. Carbuncle and the Dark Prince can also be used once they have been unlocked.

Unique to Puyo Pop is the Card Collection, a series of item delivery quests allowing the player to collect character cards of the cast. These can only be performed after the player has already beaten the normal story mode once. Once collected, the cards act as a gallery system typical of the genre, featuring artwork of the character and allowing the player to hear their voices by pressing the A button. There are 20 cards in all, with cards 19 and 20 playing music not otherwise used in the game.