Anaerobic digestion is one way to manage organic wastes by converting wastes from agriculture, industries, wastewater treatment and other human processes into energy and fertilizers (i.e. digestates). The use of digestate as fertilizer is confronted with the problematic of health risks associated with the presence of pathogenic microorganisms. Pathogens from human and animal origin present in wastes can contaminate the digestate because of insufficient elimination of pathogens during anaerobic digestion and regrowth of surviving pathogens. Consequently, the valorisation of digestate is difficult, particularly regarding land spreading. Little is known on the survival of pathogens during storage and land spreading, especially with respect to biotic and abiotic factors determining the decay of pathogens. This study aims at investigating the factors that influence the survival of pathogens during the storage of digestates to improve the anaerobic digestion process and the agricultural valorisation of digestate. Digestates from agricultural wastes were analysed. The digestates originated from different digestion processes and are representative for the French anaerobic digestion sector. The digestates were inoculated with three pathogenic bacteria, which are among the most frequently reported in agricultural wastes: Salmonella enterica, Listeria monocytogenes and Campylobacter coli. The inoculated digestates were monitored in microcosms for 40 days under conditions simulating the storage (at 24°C, without shaking and in anaerobic conditions). The pathogens and E. coli, commonly used as indicator, were monitored using culture methods and quantitative PCR. The results showed a strong decay of C. coli (not detected anymore after 7 days) and S. enterica (survived up to 20 days) regardless the microcosm. In contrast, L. monocytogenes had not the same behaviour for all microcosms and was still detected after 40 days in some digestates. The survival of pathogens seemed to be different between digestates and between pathogenic strains, suggesting the important role of biotic and abiotic factors on the survival of pathogens. The survival of the studied pathogens has been analysed in regards to the bioavailability of organic matter and microbial activity and diversity. These results will permit to characterise the properties of digestates leading to favourable conditions for the reduction of the health risks associated with pathogens.