Puzzle Kingdoms is a RPG game using tile matching mini-games as the combat system of the battles, in a similar fashion to Puzzle Quest, another puzzle-based RPG with fantasy themes released in 2007 by the same developers. Instead of swapping adjacent tiles to create groups of three or more like in the earlier title, the main gameplay mechanic this time is to move columns and rows to match tiles.
The player controls a hero character, moving between waypoints in an isometric map similar to the ones found on the Heroes of Might and Magic series. The game is divided in campaigns, where the objective is to invade and defeat all the main cities from a kingdom to conquer it. The hero character levels up automatically after winning a number of battles, adding new abilities and fresh spells to the available arsenal.
The battle screen has a grid of tiles occupying most of the central space, with the troops of the two fighting armies lined up at the sides. Each row and column has buttons to move them, and the combatants take turns trying to make matches of three or more of the same type to charge their troops and increase the damage against the enemy when attacking. When one of the troops is fully charged, an attack button lights up at the top of the screen to unleash an assault against the opposite forces. Attack tiles have a similar effect, starting the maneuver when three or more of them are lined up on the grid.
The troopers have attack and defense statistics that determine the outcome of the attacks, with the alignment with the board colors and terrain effects increasing or decreasing their points. The player can retreat, a useful strategy when the battle is practically lost, allowing the remaining troops to be saved. There are four slots below the troop lines for spells, that can be used to change the number of specific tiles on the grid, alter statistics and help in other ways. They are charged by making matches with tiles of their colors.
New troops can be recruited on the outposts, with money received after winning the battles. Shrines, taverns, dungeons and other special buildings have mini-games, with multiple goals like clearing the grid on a set number of turns, making a series of matches within a time limit and other similar challenges. Completing these bonus stages gives new items and upgrades.