- In "The Order of the Stone", Skeletons are among the few Hostile Mobs which attack Jesse and Reuben (Pig) in the forest. A Skeleton is also seen riding a minecart in the Nether Minecart System.
- In "Assembly Required", Skeletons can be seen if Jesse chooses the leave the Temple at night.
- In "The Last Place You Look", there are skeletons in Soren the Architect's Mob Grinder.
- In "A Block and a Hard Place", Skeletons can be seen running away from the Wither Storm and later in the swamp.
- In "Order Up!", Some skeletons fall down from Sky City to their deaths when Jesse and Isa are on the land below. They can be seen attacking the citizens after Jesse and Isa climb back up.
- In "A Portal to Mystery", Skeletons can be seen outside The Mansion and attack Jesse's Gang.
- In "Access Denied", many Skeletons are mind-controlled by PAMA.
- In Minecraft, sometimes a Skeleton may spawn on a Spider, making a Spider Jockey.
- Another version of the skeleton, the Stray, spawns only in snow biomes. These appear in Giant Consequences.