Anaerobic digestion is a viable on-site treatment technology for rich organic waste streams such as food waste and blackwater. In contrast to large-scale municipal wastewater treatment plants which are typically located away from the community, the effluent from any type of on-site system is a potential pathogenic hazard because of the intimacy of the system to the community. The native concentrations of the pathogen indicators Escherichia coli, Clostridium perfringens and somatic coliphage were tracked for 30 days under stable operation (organic loading rate (OLR) = 1.8 kgCOD m−3 day−1, methane yield = 52% on a chemical oxygen demand (COD) basis) of a two-stage laboratory-scale digester treating a mixture of food waste and blackwater. E. coli numbers were reduced by a factor of 106.4 in the thermophilic stage, from 107.5±0.3 to 101.1±0.1 cfu 100 mL−1, but regenerated by a factor of 104 in the mesophilic stage. Neither the thermophilic nor mesophilic stages had any significant impact on C. perfringens concentrations. Coliphage concentrations were reduced by a factor of 101.4 across the two stages. The study shows that anaerobic digestion only reduces pathogen counts marginally but that counts in effluent samples could be readily reduced to below detection limits by filtration through a 0.22 µm membrane, to investigate membrane filtration as a possible sanitation technique.