Much of the global population lacks access to basic public sanitation, energy and fertilizers. Micro-scale anaerobic digestion presents an opportunity for low-cost decentralized waste management that creates valuable co-products of renewable energy and organic fertilizer. However, field-based assessments of system performance and clearly articulated guidelines for digestate management and field application are needed. Feedstocks and effluent from seven digesters in Kampala, Uganda were monitored for standard wastewater and fertilizer metrics including indicator organisms (Escherichia coli and fecal coliform), chemical oxygen demand (COD), biological oxygen demand (BOD5), total Kjeldahl nitrogen (TKN), total phosphorous (TP), heavy metals, pH, temperature and total solids (TS) over 2 yr. Results reveal that digester effluent does not meet standards for wastewater discharge or international safety standards for field application. Data indicate that digestate could be a suitable source of fertilizer (TKN = 1467 mg L−1, TP = 214 mg L−1) but poses issues for water quality if not managed properly (TS = 26,091 mg L−1, COD = 3471 mg L−1 and BOD5 = 246 mg L−1). While effluent from the digester contained pathogen indicator organisms (fecal coliform = 8.13 × 105 CFU/100 ml, E. coli = 3.27 × 105 CFU/100 ml), they were lower than the influent concentrations, and lower than reported concentrations in drainage canals. All digestate samples contained little to no heavy metals suggesting effective source separation. Data suggest that micro-scale biogas systems have potential to improve waste handling and meet standards associated with fertilizer application with proper post-digestion treatment.