Pokémon Trozei! has gameplay similar to both Tetris and Yoshi's Cookie. The blocks are symbols shaped like various Pokémon. These blocks fall onto both screens; however, only the blocks on the bottom screen can be moved and matched. The player can move the blocks to the left and right, and the Pokémon that was moved off the edge of the screen returns to the opposite side of the screen. The blocks can also be moved downward, and the blocks on the bottom will fall to the top of the column. The blocks can be moved upwards, but will immediately fall back down if a match is not made. If four of the same Pokémon are in a row, a match is made and those Pokémon will disappear.
After a match of four is created, a Trozei Chance (or Link Chance) Icon will come up. When that happens, match-ups of three Pokémon are allowed for a short amount of time, normally two seconds. If a match of three is made during that time, match-ups of two Pokémon are allowed as well for as long as the player continues to make links every two seconds.