A method for heating a plurality of articles according to a prescribed heating profile is provided. The method includes heating a first test article in a small-scale microwave heating system and, based on the value of one or more parameters determined during this small-scale heating, determining a prescribed heating profile for the test article. Suitable parameters can include for example, net power discharged, sequential microwave distribution, average temperature and flow rate of the fluid in the heating chamber, and residence time. The heating profile can then be used to control a commercial-scale microwave heating system used to heat a plurality of similar articles.