As for other renewable energies in Germany, biogas production has rapidly expanded in recent years, such that the current installed capacity in this country accounts for around half of the European total. Against this background, and recognising the actual research need in the profitability analysis of along the whole supply chains for biogas, this paper carries out an economic analysis of three operational German co-digestion biogas plants, which employ biowaste, sewage sludge and energy crops for electricity production as well as for injection of biomethane into the natural gas grid. The profitability of the considered plants is assessed using the static Profit Comparison and the dynamic Net Present Value methods. From the analysis of each of the plants based on several technical and economic assumptions, the production costs for electricity and biomethane have been derived. Investment-related costs and substrate prices represent the most important financial variables of the considered plants. The electricity production from energy crops appears to be the most lucrative option, with a dynamic pay-back period of 6.7 years. Hence, subsidies and incentive schemes for biogas play a key role for the plants using energy crops as well as for plants using biowaste and sewage sludge. Furthermore, process failures under mesophilic conditions are here briefly described and could affect the biogas yield and thus have an influence on the profitability of the plants. The obtained results represent the foundation for a forthcoming comprehensive energy system analysis of the integration of biogas into the German energy system.