In our study, we monitored the inactivation of two important viruses that are critical in animal husbandry throughout the world. To evaluate the influence of the composting process on inactivation of avian influenza virus (H9N2) in poultry manure compost (PMC) and Encephalomyocarditis virus (EMCV) in pig (swine) manure compost (SMC), the H9N2 and EMCV were injected in dialysis cassettes and buried in two different manure compost piles of poultry and pig manure, respectively. The highest temperature achieved in the PMC and SMC piles during the test period were 75 °C and 73.5 °C, respectively. At the completion of the composting for 168 h, inactivation effect appeared to be more sensitive in H9N2 than EMCV. The vitality of H9N2 decreased by 6.25 ± 0.35 log10TCID50/mL to 0.0 log10TCID50/mL within 1 h of the composting. The vitality of EMCV decreased from 7.75 ± 0.35 log10TCID50/mL to 1.50 log10TCID50/mL within 24 h of starting the composting process. However, the activation of EMCV was not decreased (from 7.75 ± 0.35 to 7.50 ± 0.71 log10TCID50/mL) in the control treatment (not inserted in composts) after 168h, while the activation of H9N2 in dialysis cassettes was significantly decreased (from 6.25 ± 0.35 log10TCID50/mL to 2.00 ± 0.6 log10TCID50/mL). Our study demonstrated the effectiveness of the composting treatment in inactivating the viruses studied, which was not the case with air treatment.