Subterranea is a side-scrolling shooter in which players must guide a ship through 16 caves. Various enemy formations attack the ship and must be dodged or destroyed. Most caves contain narrow passages that are difficult to navigate, as well as destructible walls and gates that must be opened by shooting small control boxes. The ship's weapon cannot be powered up and there are no end of level bosses. In between stages, "guardians" can be destroyed for extra lives. Guardians constantly fill the screen with bubbles. In order to destroy a guardian, all glowing bubbles must be shot. If the guardian isn't destroyed, the player is still taken to the next level, but doesn't receive an extra live.