Domestic and imported biomass or biofuels used for energy purposes play an important role in many future energy scenarios and national policies. But both the realizable potential for biomass and the environmental consequences of its deployment for energy can be controversial. The aim of this study is to identify environmentally-optimal strategies for bioenergy, considering domestic biomass resource availability, the full energy system context, and a consequential life cycle perspective. We apply our approach to the case of Switzerland and three alternative energy scenarios for the year 2035, and compare the environmentally-optimal strategies obtained over several single-issue and one fully-aggregated impact indicator. From the optimal solutions, we analyze substrate-specific (i.e., per biomass resource type) marginal impacts of biomass supply and the influences of boundary conditions imposed on biomass use by the different future energy scenarios. Minimizing impacts on global warming, cumulative fossil energy demand, and the Swiss ecological scarcity method leads to near-complete utilization of sustainably-available biomass resources, whereas less biomass is deployed when optimizing for particulate matter formation, land use (biodiversity loss), and water footprint. The results suggest that increased deployment of energy wood (excluding forest wood apt for material applications) and manures would be environmentally beneficial. In contrast, substrates suitable for animal feeding should not be used for energy purposes due to the burdens associated with increasing the demand for conventional feed-stuffs. The findings and case-specific recommendations illustrate the importance of considering a holistic environmental perspective, alongside techno-economic restrictions to the physical biomass potential, when establishing national (bio-)energy policies.