Livestock manure is a major source of pathogens (eg, foot and mouth disease–FMD) and pollutants, in addition to odors from microbial degradation of organic matter. In this study, the feasibility of a Thermophilic Aerobic Oxidation (TAO) method for the treatment of Encephalomyocarditis virus (EMCV) in swine manure was investigated in reference to a classical alkaline method. In the course of this study, relative performance of two treatments was also tested against chemical oxygen demand (COD) and nutrient reduction. The TAO and alkaline method reduced total kjeldahl nitrogen (TKN) concentration by 52% and alkaline method 23%, respectively. In the case of NH4–N, they reduced 67 and 11%, respectively. Similarly, the former also reduced the EC significantly compared to the latter. Based on this study, deactivation of the EMCV by the alkaline treatment system reduced EMCV by the latter approached 99.97% within an hour, whereas the former did the same a little slowly (by 3 hours). The overall results of our study suggest that TAO method is equally good or better than the alkaline method in treating infected manure to reduce microorganisms to an acceptable level. Thus, TAO system is considered an appropriate alternative to the alkaline treatment method for hygienic management of livestock manure.