There are many types of monsters in Lyoko. Xana creates them in order to keep the towers it activates safe. Some are a mere nuisance while others are a major threat. The ones that can be considered a nuisance make up for this fact by travelling in packs. All of them, however, try to impede the group. The monsters remain until they are destroyed or a return trip is activated. Xana has eleven types of monsters so far. Odd, Ulrich and Yumi each have special weapons in Lyoko in order to destroy the monsters. Aelita mostly relies on the protection of the others when it comes to dealing with the monsters in the first two seasons, but gains a weapon in the third.

Other monsters exist that don't fall into the same category as Xana's monsters. One is a monster Jeremy produced, called the Marabounta. It appears in only one episode. There is also an entity known as the Transport Orb. It's a giant white sphere with an Eye of Xana printed on it, like all of Xana's monsters. Unlike the other monsters, however, its only purpose is to ferry passengers from the edge of any region to the center of the fifth sector, Carthage, and back again. Both Jeremy and Xana can access it at will. This entity's classification as a monster is arguable, but it is included for the sake of completion.

Also, there are monsters, located in the digital sea. These monsters must be destroyed using torpedoes shot from the Skidbladnir or Nav Skids.