Agricultural anaerobic digestion is a booming business in Europe. The digestate, solid product of the methanization used as a fertilizer, is intended to be spread on agricultural land. It is therefore important to ensure the safety of the digestate from a health point of view. The inputs and products of an agricultural biogas plant have been characterized microbiologically. The study demonstrated that anaerobic digestion has no impact on Clostridium perfringens. However, anaerobic digestion led to a reduction in the concentration of certain pathogenic bacteria such as Escherichia coli or enterococci.