Abstract Waste streams such as municipal wastewater and animal manure contain organic materials and nutrients that can be converted and recovered for bioenergy and renewable fertilizer production. In the first part of this thesis, the anaerobic co-digestion of dairy manure with kitchen waste and chicken fat was studied for the purpose of increasing biogas production. The methane yields of co-digestion substrates mixed at different ratios were determined by bio-methane potential tests. The highest methane yield, which was 114% higher than the baseline, was observed when dairy manure was mixed with kitchen waste and chicken fat at the ratio of 1:2:2 (volatile solids based). The mixed substrates were then fed to a lab-scale continuous stirred-tank reactor. The co-digestion was stable and biogas production was 1559�195 mL biogas/L·day at organic loading rate as high as 6.8g COD/L*day. In the second part, a new approach was proposed for phosphorus removal and recovery from wastewater. Nine strains were identified to have the capability of high phosphorus removal and storage comparable to Polyphosphate Accumulating Organisms (PAOs) in the Enhanced Biological Phosphorus Removal (EBPR) process. Batch experiment using synthetic wastewater showed that <italic>Mucor circinelloides</italic> can remove ~ 72-82% phosphorus when P to COD ratio was roughly 1:100. The phosphorus recovered from wastewater in the form of polyphosphate-containing fungal biomass could be used as fertilizer, providing a potential alternative to biological nutrient removal and a solution to sustainable agriculture.