Oddworld: Munch's Oddysee is set in the fictional Oddworld universe and take place after those of Abe's Exoddus. The player controls Munch as well as Abe, the hero of the previous Oddworld games. Abe's abilities haven't changed much since the last installment: as before, GameSpeak must be used to communicate with other creatures, leading them to safety. His fellow Mudokons can now be ordered to attack enemies. Abe can also grab and toss Mudokons or Munch to lead them to area they cannot access otherwise. Possessing enemies also comes into play, and is needed to solve many of the puzzles. Possession abilities can now be used to ignite quarrels between enemies and make them fight each other.

The player can change between Abe and Munch instantly throughout most of the game. Munch brings on the table new abilities of his own: he can use his sonar to control or immobilize specific creatures, as well as swim. Another new addition is the possibility to use vending machines, which sell various items that enhance the abilities of the protagonists. At certain points Abe and Munch can also remote-control mechanical creatures.

Munch is the last surviving Gabbit living on Oddworld after their poaching to the verge of extinction. And now the greedy, vile Vykkers Labs have big plans for their fortune and glory through his doom. Meanwhile, veteran Oddworld saviour and outlaw Abe learns he needs Munch's help to save his species from industrial atrocity and vice versa. In an all new 3D oriented world using familiar gameplay, travelling through military bases, factories and the natural world, the two must work together and succeed together to lead the oppressed natives to freedom, decommissioning local police forces and shutting down industrial pollution in order to return balance to Oddworld.