Looking for renewable energy sources is one of the main targets in the transition to low-carbon economies. Bioenergy appears as an alternative with great potential, but firstly, it requires addressing all aspects that can limit its environmental viability. Stillage has been identified as an environmental concern of the bioethanol production. Thus, eco-friendly strategies for valorizing this resource should be pursued. In this work, three strategies such as composting (non-energy valorization), one-stage anaerobic digestion (with the aim of biogas production), and dark fermentation followed by anaerobic digestion (scheme under development to produce biohydrogen and biogas) were evaluated under a life-cycle perspective; and through process modeling based on literature data. The aim is to identify the advantages and disadvantages of dark fermentation for the management of apple stillage. To do this, a cradle-to-gate and attributional framework were followed, considering impact and damage perspectives. Results showed a very significant environmental load (around 99%) of composting compared to the selected energy recovery schemes, considering the added value of compost and the associated emissions versus those of biofuels. Otherwise, small differences were found between single-stage anaerobic digestion and dark fermentation (up to 16%), mainly, due to changes in chemical consumption and organic matter degradation efficiency. Display omitted •Stillage valorization strategies from the apple distillery industry were analyzed.•Environmental benchmarking of composting, anaerobic digestion and dark fermentation.•Energy demand and direct emissions were the hotspots in all scenarios evaluated.•Close performance for anaerobic digestion and dark fermentation in midpoint impacts.•Dark fermentation process reaches an emission of 0.15 kg CO2eq per kg of H2 produced.