A programmable control system for a cooking apparatus having a housing defining a cooking chamber with one or more food transport conveyors traveling there-through between opposing cooking elements. A food probe is provided for insertion into cooked food items to ascertain the internal cooked temperature and a control program to automatically call for the probing of temperature readings of food items on a predefined schedule, and to record the temperature readings. The control program also compensates for temperature degradation when the apparatus is under significant cooking loads. The control program also compensates for the malfunction in the cooking elements, wherein if one cooking element on one side of the conveyor path malfunctions, a corresponding heating element on the opposite side of the conveyor is deactivated and simultaneously the conveyor speed is slowed to compensate for the reduction in heating to maintain balanced cooking of the food.