An in-line shell egg pasteurizer has a clean-in-place system. Empty shell egg carriers are placed in the water bath for multiple cleaning cycles. The cleaning solution level is lowered to expose the shell egg carriers and the top parts of the water bath walls. An air perturbation is used to agitate cleaning solution held in the bottom of the water bath and clean heating coils and other components located in the bottom of the water bath. Sprayers (e.g., nozzles, cleaning spray balls, etc . . . ) mounted on a hood over the water bath clean the top parts of the water bath walls and the empty shell egg carriers placed in the water bath.