A method for controlling a microwave heating system is provided. The method may be used with a system having a liquid-filled microwave heating chamber and includes measuring the value of one or more microwave system parameters. Suitable parameters can include, for example, net microwave power discharged, the temperature of the liquid in the microwave chamber, the flow rate of liquid through the microwave chamber, and the speed of the conveyance system disposed within the microwave chamber. The measured value of the selected parameter is then compared to a target value for that parameter in order to determine a difference. Based on the difference, one or more actions can be taken in order to start, stop, or alter the operation of the microwave heating system.
