Small-scale anaerobic digestion of wet organic wastes can make positive contributions to climate mitigation, energy security and nutrient cycling in agri-food systems. However, the environmental sustainability of small-scale anaerobic digestion is undermined where lack of capacity to utilize the biogas fuel results in biomethane venting to the atmosphere, contributing to climate change. Policy support for improved manure management in Bali, Indonesia, has resulted in the installation of small (6 m3) anaerobic digesters across 752 Bali cattle breeding units. These 752 remote rural digesters annually vent approximately 75 482 ± 37 741 m3 of biomethane into the atmosphere as a waste, owing to lack of practical means to convert this potential fuel into useful energy. Meanwhile, most of these cattle farms lack access to electricity. This paper describes the performance of a novel, compact and versatile “BioMiniGen” system that provides convenient electricity generation from small-scale biogas production. This innovative system comprises: (i) a simple biogas desulfurizing system; (ii) a two-stroke, single cylinder (63 cc) air-cooled engine; (iii) an electric generator; (iv) an optional CO2 removal unit. Lifecycle assessment indicated that bioelectricity generated by the BioMiniGen would have a smaller environmental footprint than Indonesian grid electricity across 11 impact categories, including a negative global warming burden owing to avoidance of biogas venting. Trade-offs included a larger abiotic depletion burden associated with manufacture of the generators. Over a five-year lifetime, each unit, costing US$500, could generate up to 5971 kWh of electricity and mitigate up to 65.1 Mg CO2 eq., with a greenhouse gas abatement value up to US$13023. Across Bali, up to 898 ± 449 MWh yr−1 bioelectricity could be generated, and 1.92 ± 0.96 Gg CO2 eq. saved. Further pilot trials are needed to ascertain realistic biogas yields from cleaned digesters managed for bioenergy generation alongside manure management. BioMiniGen technology could make an important contribution to energy security for the 1.4 billion people globally who lack access to electricity.