Processes and systems that enhance the heating of packaged foodstuffs and other items in various microwave heating systems are described herein. It has been unexpectedly found that configuring the microwave heating zone of a microwave-assisted pasteurization or sterilization system so that the article carrier, the microwave launchers, and/or the packages have certain relative dimensions may significantly enhance the uniformity of heating of the articles. The result is pasteurized or sterilized articles that exhibit fewer hot and cold spots, a consistent microbial lethality rate, and desirable end properties, such as visual appearance, taste, and texture.