A self-cleaning system for a convection cooking appliance controls the activation and deactivation of multiple heating units, as well as a blower, throughout an initial preheat and subsequent phases of a cleaning operation. More particularly, at least first, second and third heating units are provided, with two of the units being positioned in an air channel assembly which extends about at least a portion of the oven cavity and the remaining heating unit being positioned within the oven cavity. The heating units in the air channel assembly are activated, along with a blower, during a preheat phase to heat the oven cavity at a controlled rate, while developed byproducts are directed through a catalyst. Following the preheat phase, the blower and one of the heating units in the air channel assembly are deactivated, while the heating unit in the oven cavity is activated to rapidly increase the temperature of the oven cavity.