Nazo Puyo (Secret Puyo) takes the "Quest mode" found in many Puyo Puyo games and breaks it off into a game of its own. Whereas the usual Puyo Puyo gameplay is centred around beating an opponent by having a more skillful play technique, the puzzle mode (and all Nazo Puyo) games is a leisurely puzzle game where you have to fulfill a set goal on a screen already filled with a certain arrangement of Puyos.

These goals may be to simply eliminate all Puyos on-screen, to eliminate all Puyos of a certain colour, or to eliminate a certain number of Puyos at once. You may also be asked to do a "rensa", or chain reaction, in a certain number of steps. A "rensa" is arranged by making so that if one set of four or more Puyos is eliminated, it will make neighbouring Puyos fall so that new combinations arise, and are eliminated. The fulfillment of the goals may be complicated by the fact that you are given only Puyos of a certain colour to work with.

The game has also an edit mode, where you can make your own puzzles given all the options described above.