Appropriate treatment of agricultural waste is necessary for the protection of public health in rural areas because land-applied animal manure may transmit zoonotic disease. In this study, we evaluated the potential of using a pilot anaerobic membrane bioreactor (AnMBR) to treat agricultural waste. The AnMBR system, following a conventional complete mix anaerobic digester (CMAD), achieved high removals of biological and chemical agents. The mean log(10) removals of Escherichia coli, enterococci, Clostridium perfringens, and coliphage by the AnMBR were 5.2, 6.1, 6.4, and 3.7, respectively, and for the CMAD were 1.5, 1.2, 0.1, and 0.5, respectively. Compared with other indicators, coliphage was observed most frequently and had the highest concentration in effluent samples. Bovine adenoviruses and bovine polymaviruses (BPyV) were monitored in this study using nested PCR methods. All of the CMAD influent and CMAD effluent samples were positive for both viruses, and three AnMBR effluent samples were BPyV positive. The mean removals of total Kjeldahl nitrogen, total phosphate, chemical oxygen demand, total solids, and volatile solids by the entire system were 31, 96, 92, 82, and 91%, respectively, but there was no removal of ammonium. When the AnMBR was operated independent of the CMAD, AnMBR achieved similar E. coli and enterococci removals as the combined CMAD/AnMBR system. The high quality of effluent produced by the pilot AnMBR system in this study demonstrated that such systems can be considered as alternatives for managing animal manure.