The present invention relates to a method and system for treating waste materials, such as wastewater treatment plant biosolids or process wastes, by application of energy waves. In one embodiment, waste materials are treated by adding and blending an alkaline material to the waste material, and applying energy waves, such as microwaves or radio frequency waves, thereby significantly reducing pathogenic microorganisms in the waste material to meet the requirements of 40 C.F.R. 503 (2002) for producing a Class “A” product for beneficial use.