Bioenergy is a building block of the ongoing transformation toward renewables-based energy systems. Bioenergy supply chains are regionally embedded and need to be seen in a place-based context with specific characteristics and constraints. Using a German case study, the potential of regionally embedded bioenergy chains in the past and the future is analyzed and discussed in this paper. The analysis integrates socio-ecological data and applies sustainability criteria in a multi-criteria decision analysis (MCDA) using the Preference Ranking Organization Method for Enriched Evaluation (PROMETHEE) methodology. The case study is focused on an industrial biogas fermenter in northwestern Germany, which currently uses predominantly maize as a substrate for bioenergy. Objectives for future development according to the ambitions of the UN Sustainable Development Goals and the EU Renewable Energy Directive (RED II) discussion are set and include the involvement of the farmer as biogas plant operator and other regional stakeholders. Since the focus of the research is put on the contribution of alternative biomass, such as grass, for the optimization of bioenergy settings, the question concentrates on how different mixtures of alternative biomass can be embedded into a sustainable management of both the landscape and the energy system. The main findings are threefold: (i) bioenergy supply chains that involve alternative biomass and grass from grasslands provide optimization potentials compared to the current corn-based practice, (ii) with respect to more sustainable practices, grass from grassland and alternative bioenergy supply chains are ranked higher than chains with increased shares of corn silage, and, more generic, (iii) optimization potentials relate to several spheres of the social–ecological system where the bioenergy structure is embedded. To conclude, sustainable enablers are discussed to realize optimization potentials and emphasize the integration of regional stakeholders in making use of alternative biomass and in making regional bioenergy more sustainable.