Bubble Bobble Evolution takes the classic platforming gameplay that defined the originals and expands it into entirely new realms by injecting all manner of innovations, from new bubble types to new environmental hazards and puzzle elements. Its Story Mode retells the classic story of two human brothers trapped in bubble-blowing dinosaur bodies by an evil nemesis, only this time the action takes place in two "Towers of Entertainment", cylindrical sections of which form the game's levels.

The first new feature comes with the level structure itself. Gone is the classic static structure of Bubble Bobble and in its place are three screens on a central 'spindle', which the player can move between at will.

Contained within these screens are the basic elements of Bubble Bobble gameplay: The monsters and the bubbles. However, progress is no longer a simple issue of dispatching the wandering monsters to advance onward.

New puzzle elements now hinder the player, bringing an entirely new dynamic to the classic Bubble Bobble gameplay. By using the basic techniques refined over a decade of Bubble Bobble titles, players must overcome a cerebral challenge in each level. These can take various forms of elemental exchanges, such as finding a source of fire to melt an ice barrier, or watering a seed so it can grow to fill a gap left by a missing platform.