The present invention generally provides a method and apparatus for cleaning a showerhead of a deposition chamber, such as a metal organic chemical vapor deposition (MOCVD) chamber. In one embodiment, the showerhead is cleaned without exposing the chamber to the atmosphere outside of the chamber (i.e., in situ cleaning). In one embodiment, flow of liquid coolant through a cooling system that is in fluid communication with the showerhead is redirected to bypass the showerhead, and the liquid coolant is drained from the showerhead. In one embodiment, any remaining coolant is flushed from the showerhead via a pressurized gas source. In one embodiment, the showerhead is then heated to an appropriate cleaning temperature. In one embodiment, the flow of liquid coolant from the cooling system is then redirected to the showerhead and the system is adjusted for continued processing. Thus, the entire showerhead cleaning process is performed with minimal change to the flow of coolant through the cooling system.