Water, sanitation and hygiene interventions are among the most significant health interventions addressing the worldwide burden of diarrheal disease and environmental enteropathy. Sanitizing human excreta and animal manure (HEAM) is a critical step in reducing the spread of disease and ensuring microbially safe reuse of waste materials. From the perspective of human excreta, it was recently established that despite an increase in global toilet coverage, the proportion of safely managed fecal waste remains low. Therefore, on-site storage and treatment still represent the best opportunities to reduce pathogen load. Among these pathogens, viruses are particularly persistent. However, adequate storage or digestion of HEAM can strongly reduce the number of viruses by creating adverse conditions to their survival. Although temperature, pH and ammonia (NH3) are commonly reported as primary virus inactivation factors, the mechanisms underlying virus reduction remain unclear. This thesis aims to shed more light on these mechanisms and their exploitation for HEAM management. Overall, this work provides a better comprehension of the mechanisms underlying virus inactivation during human excreta and animal manure treatment. It allowed establishing a comprehensive prediction model forMS2 inactivation in HEAM, which is made available on the internet. Finally, this thesis offers a simple decision making tool to optimize virus inactivation during storage and treatment of human excreta and animal manure.