Puyo Puyo is a puzzle game with two players, although one may be controlled by the computer. Pieces come down in pairs, sometimes of different colors. When players connect at least four pieces, they "pop" those pieces, making them disappear. Two pieces are "connected" when they touch horizontally or vertically but not diagonally. Pieces that were above the popped pieces then fall down to fill the void created. The falling pieces can then create a connection of four similar colored pieces, thus causing a chain.

When the player successfully pops pieces, they send "garbage" pieces are the opposing player, falling from random columns. The more pieces in a pop and the longer the chain, the more pieces are sent. These garbage pieces are uncolored and do not chain but if they are adjacent (again, vertically or horizontally but not diagonally) to a popped colored piece, then they also disappear.

The player that hits the top of the well loses.