Nazo Puyo 2 continues where the original left off. It contains 200 new puzzles to solve, compared to the 100 of the predecessor. Each puzzle is played Puyo Puyo-style, but with a certain goal to complete using a preset set of puyos, e.g. "destroy all puyos", "eliminate 9 puyos at once", "make a triple combo" and so on, thereby taxing players' Puyo Puyo skills and strategies.

Another new addition is a battery backup, allowing players not only to save their current position, but also to save all puzzles that may have been created in the edit mode.