The energy efficiency of different biogas systems, including single and co-digestion of multiple feedstock, different biogas utilization pathways, and waste-stream management strategies was evaluated. The input data were derived from assessment of existing biogas systems, present knowledge on anaerobic digestion process management and technologies for biogas system operating conditions in Germany. The energy balance was evaluated as Primary Energy Input to Output (PEIO) ratio, to assess the process energy efficiency, hence, the potential sustainability. Results indicate that the PEIO correspond to 10.5–64.0% and 34.1–55.0% for single feedstock digestion and feedstock co-digestion, respectively. Energy balance was assessed to be negative for feedstock transportation distances in excess of 22 km and 425 km for cattle manure and for Municipal Solid Waste, respectively, which defines the operational limits for respective feedstock transportation. Energy input was highly influenced by the characteristics of feedstock used. For example, agricultural waste, in most part, did not require pre-treatment. Energy crop feedstock required the respect cultivation energy inputs, and processing of industrial waste streams included energy-demanding pre-treatment processes to meet stipulated hygiene standards. Energy balance depended on biogas yield, the utilization efficiency, and energy value of intended fossil fuel substitution. For example, obtained results suggests that, whereas the upgrading of biogas to biomethane for injection into natural gas network potentially increased the primary energy input for biogas utilization by up to 100%; the energy efficiency of the biogas system improved by up to 65% when natural gas was substituted instead of electricity. It was also found that, system energy efficiency could be further enhanced by 5.1–6.1% through recovery of residual biogas from enclosed digestate storage units. Overall, this study provides bases for more detailed assessment of environmental compatibility of energy efficiency pathways in biogas production and utilization, including management of spent digestate.