Against the background of a rapidly developing German biogas to electricity sector, this paper identifies the most profitable biogas plant configurations under the current energy-political framework conditions, by considering variable biomass inputs and prices. The paper addresses the following research question: what is the optimal biomass input to be valorized, in order to maximize the specific net operating profit of the considered plants? For the considered supply chains, i.e. energy crops with manure and biowaste valorization, kinetics as well as biological reactions are considered in order to model the biogas production. In a further step, an economic assessment for the two biogas plant types is realized by determining the annual costs, as well as by considering subsidies for the electricity generation from biogas based on the German Renewable Energy Sources Act 2012. For each of the two considered supply chains, an optimal economic operation point is determined, regarding the valorized biomass input quantity. In the case of a co-digestion from energy crops and manure, 4.32 ct/kWh_el are reached for an optimal installed capacity of about 1.2 MW_el. Biowaste plants show a theoretical maximal specific net operating profit of 4.97 ct/kWh_el at about 4.0 MW _el with biowaste subsidies at 50 €/t and for 120,000 t/a valorized substrate. Whilst agricultural plants are generally more economically attractive they exhibit a higher greenhouse gas potential, which means a trade-off. The successful future development of the German biogas sector will thus rely on overcoming several technical, social and political barriers.