According to example embodiments, there is provided a method of cleaning a semiconductor device manufacturing apparatus. In the method, a fluorine-containing gas is provided into a chamber to clean a byproduct formed on a surface of a chamber during formation of a layer structure therein. A material is provided into the chamber to chemisorb the material on the surface of the chamber. The material is substantially similar to or the same as a source gas for forming the layer structure. A plasma is generated in the chamber, and the chamber is purged.