Mission Minigames are games within the Super Moshi Missions that take place in their own realm. They are introduced with their title, require clicking to proceed and have their own assets and music.
Door PuzzleMissing Moshling Egg. To gain access to Dr. Strangeglove's lair, you must obtain the key from Skull Guard's head. They do not oppose this, basically dare you to, as their skull is full of Creepy Crawlies.
Poop Deck PanicVoyage Under Potion Ocean. It is one of the two tasks given to Super Moshi by Cap'n Buck who claims he cannot set sail without these tasks done. This specific task is to clean the Poop Deck of the Cloudy Cloth Clipper. One must hold their mouse button down and rapidly scrub the spots on the deck until they're gone.
Asset 70 holds various smears and graffiti by Bonkers, that would supposedly be used to make the dirt on the deck randomized in design.
Barnacle BusterVoyage Under Potion Ocean. It is one of the two tasks given to Super Moshi by Cap'n Buck who claims he cannot set sail without these tasks done. This specific task is to free the hull of the Cloudy Cloth Clipper from barnacles. You need to time when you click to fist so it is on the range of the barnacle you need to remove. There is a total of 10 barnacles.
Journey to Dr. Strangeglove's HideoutVoyage Under Potion Ocean. You need to get yourself through the ocean floor to reach Dr. Strangeglove's hideout, but it's covered in Glumps and mines. The keys are used to avoid impact and the sonar clears your way but requires loading up before launching.
Hoodoo PongooBungle in the Jungle, where Super Moshi needs to pass the ancient Hoodoo trial in order to be allowed to learn about the secret recipe to Hoodoo Stew.
It's just plays like regular Pong. A total of 3 turns are played if neither party has reached a score of 2.
Hoodoo HopBungle in the Jungle, where Woolly (who is trapped in the Zoshling Ignition Key) must run away from the angry crowd of Woolly Hoodoos.
The gameplay of this game is similar to Run, Shelby, Run!, except that it is the other way around.