- In "The Order of the Stone", zombies attack Jesse and Reuben in the forest near EnderCon. Later, they also attack Jesse/Axel (Determinant) when they come out of the Nether Portal.
- In "Assembly Required", zombies and other hostile mobs block Jesse's Gang on the way to Soren's Fortress.
- In "The Last Place You Look", zombies are seen inside the mob grinder and the loot room.
- In "A Block and a Hard Place", a horde of zombies are seen in the maze in the Far Lands.
- In "Order Up!", Jesse fights several zombies at the Temple of the Old Builders. Zombies also spawn in Sky City later.
- In "A Portal to Mystery", Jesse's Gang travel to a world full of zombies. They seem to be spawned from multiple zombie spawners located in The White Pumpkin's lair below the Mansion. Also in the dining room, a painting of a baby zombie riding a chicken can be seen.
- In "Access Denied", some zombies are mind-controlled by PAMA, and Jesse can also control a few with the Mind Control Headset.
- In "A Journey's End?", if Jesse chooses 100 chicken-sized zombies at the beginning of Episode 1, Hadrian and Mevia will be imprisoned in a world full of tiny zombies. (Not baby zombies). (Determinant)
- In "Hero in Residence", Jesse and Petra fight zombies in a mine-shaft.
- In "Giant Consequences", Romeo summons zombies and other hostile mobs when changing the time to night with the Clock. Later, Jesse's Gang has to fight zombies when Romeo traps the world in eternal snowy night.
- In "Jailhouse Block", zombies appear in the Zombie Mines, the second-to-last floor of the Sunshine Institute.
- The exclusive variant of zombie also appears, called Prison Zombies.
- In regular Minecraft, there is a low chance to spawn a zombie villager instead of a normal zombie. However, those don't appear in Minecraft: Story Mode.
- Stampy Cat repeatedly describes zombies as "googlies."
- This is a reference to the real Stampy calling monsters "googlies" most of the time in his Minecraft YouTube series.
- The only occurrence of a mob ever crafting at a Crafting Table and placing blocks in Minecraft: Story Mode is in Episode 7 where Jesse controls a zombie using the Mind-Control Headset.
- Since their skin is based on Steve's, most zombies could actually be male.