Methods for pasteurizing or sterilizing liquid or semi-liquid materials in a liquid-filled microwave heating system are described herein. The methods described herein may be used for pasteurizing or sterilizing a variety of different liquids and semi-liquids, including foodstuffs and beverages, as well as medical, pharmaceutical, nutraceutical, and veterinary liquids. Efficient and rapid heating using microwave energy can provide better temperature control, which permits the use of thinner bottles without sacrificing product quality or safety.