Puzzle Quest: Galactrix is, just like its predecessor, a mix of many different genres. At its core there is a Bejeweled-style match-3 puzzle game. In Galactrix, the gems the player has to match have been changed to hexagon shapes, making diagonal matches possible. Also, new gems are filled in from whatever side the player last removed a gem, making the gameplay even more complex.
The game's back story is this time set in the future, and the player has a large galaxy map to explore. In each star system, there are a number of planets, asteroids, leap gates and space stations. The player has to accept missions which further the background story, but they can also choose to do side quests like mining for raw materials that can be sold for varying prices in each solar system.
During the course of the game, the player can pick up several side characters which bring along with them mini games, like constructing devices for the player's ships or hacking leap gates to access new areas on the map. The core gameplay revolves around battling other space ships though. Successful battles will result in more intel (the equivalent of experience points), which in turn helps leveling up the player's hero, increasing their stats.