Gameplay in PixelJunk Monsters has similarities to various tower defense titles. The objective is to build defense towers along the enemies' path to keep them from reaching a hut, or base. Several small creatures dwell at the base. For each enemy that survives the defense towers and reaches the hut, one creature is killed. If all creatures are wiped out, the level is failed.

Towers have distinct attributes, such as rapid fire, long range, air-focused, etc. Destroyed enemies usually drop coins and occasionally give gems, which then can be used to upgrade and research new towers.