Puyo Puyo Champions also features 24 playable characters, complete with their own distinct AI behavior and Fever drop pattern, though some of these characters simply reuse the existing AI of characters not appearing in the game as playable. These characters include fan-favorites from the original Compile game series such as Arle Nadja and Dark Prince, as well as newer characters such as Ally, who debuted in the Japan-only Nintendo 3DS game Puyo Puyo Chronicle. The 2.02 update, released in August 2020, added two hidden characters, Rafisol and Paprisu, each of whom can be selected by inputting a specific button combination while selecting character.

The game also allows players to personalize their in-game profile image, with over a hundred characters to choose from both the main game series and Puyopuyo!! Quest, as well as a selection of backgrounds and borders, all of which seem to be carried over from Puyopuyo!! Quest.