Side-scrolling stages are generally presented as having an isometric perspective, while platforming stages that feature vertical progression are presented non-isometrically, which allows the player characters to crouch. Objects from the environment or enemies can also be used as weapons, such as legs from broken-apart Walkers, beaks from ravens, pipes on the wall of Intruder Excluder, and flagpoles from the Dark Queen's tower. Due to the variety of gameplay styles between stages, all attacks are only usable in certain levels. These special moves are usually activated after three or four regular punches or running at a faster pace, which is done by pressing left or right on the D-pad twice in a row followed by a B-button press that triggers the Smash Hit.

Throughout the game, the Toads are equipped with a regular punch as well as other 'Smash Hits' that can be performed against enemies: the 'Turbo Thwack', 'Swingin' Size Thirteen', 'Jawbuster', a punch with an enlarged knuckle named 'Kiss-My-Fist', a headbutt attack named the 'Battletoad Butt', 'BT Bashing Ball' which is only used while hanging on the Turbo Cable in the second level where the toad character shape-shifts into a wrecking ball, the 'Take Out the Trash', where an enemy is picked up and thrown overhead, a clasping of both hands to bash an enemy named 'Nuclear Knuckles', 'the Punt' where a 'toad repeatedly kicks an enemy after he knocks one into the ground, and a very powerful kick named the 'Big Bad Boot'. While the levels of Battletoads vary greatly in gameplay style, the game is generally presented as a 'beat'em up', in which players progress by defeating enemies while avoiding the hazards in the environment. The player has a maximum of six hit points that can be replenished by eating flies. The game contains no saving system or password features. Players start with three lives each time the game is started, which get replenished every time the player continues after getting defeated. The game is a platform scrolling beat 'em up, with varying elements of racing, climbing and vehicle-based obstacle courses.

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