Pokémon Puzzle Collection brings together four varieties of brain teasers, each themed around the world of Pokémon. Three modes — Shadow Puzzle, Motion Puzzle, and Rescue Mission — are available from the start, with a fourth mode called Power On unlocking after thirty puzzles have been solved. Each category contains twenty puzzles divided into five difficulty levels, with four puzzles per level. Harder levels demand sharper thinking, and every solved puzzle adds the featured Pokémon to the in-game Minidex, offering a secondary goal for completionists.