Mr. Runch is a rotten and dangerous peanut that has escaped the reject bin. Burning with revenge and sworn to become a real M&M peanut, he is now on the loose and plans to kidnap all M&M's to lock them up in a crystal. Five M&M heroes - Red, Yellow, Blue, Green and Orange - need to stop him.

M&M's Break' Em is mainly a reworking of Gem Smashers, an earlier game by Frame Studios Interactive. The main story mode takes place on different locations, gradually unlocked, along with boss battles. Keys can also unlock hidden levels, marked by a pink spot on the map.

The player controls one of the M&M's and bounces it throughout the screen. They have different characteristics such based on speed, power and boost. It needs to hit crystals of the same colour (pinballing vertically off objects) and special pots are used to change the colour. When all crystals are gone, the level is completed. Gameplay is time limited, crossing it makes a bouncing skull appear on the screen taking away lives. Special blocks contain bonuses such as detonators, extra points, invulnerability, score multipliers and a harder M&M that cuts through all crystals. The M&M can be moved left or right horizontally, and sped up or slowed down.

Skills slightly influence gameplay. High power requires less hits to break hard rocks, while boost allows the character to speed up. Only Yellow and Green can break special blocks to access bonuses.

The DS version can be controlled with the stylus and contains a multiplayer mode.