The core gameplay of Lego Batman 3: Beyond Gotham is very similar to that of the two previous Lego Batman games: Lego Batman: The Videogame and Lego Batman 2: DC Super Heroes. The player controls any one of a wide assortment of characters (of which there are over 150[6]) from a third-person perspective, primarily fighting enemies, solving puzzles, and collecting Lego 'studs', the game's form of currenccy. Using attack combinations in combat will multiply the number of studs earned. Up to two players can play in co-operative mode.[7]

There are many different environments in the game. All are based on DC comics' universe's locations. As in previous Lego video games, levels are unllocked for 'Free Play' mode once they are completed in Story Mode. 'Free Play' allows the player to replay any level they have completed, but with any characters they have unllocked so far. This permits access to special areas containing additional collectables, that the player was unable to get to before. This is unlike Story mode, in which the player may only switch between the preset characters involved in that scene