AbstractCover crops offer a potential biogas feedstock, and to enable continuous operation of the biogas plant, ensiling can be used for biomass preservation. The aim of the present study was to assess the environmental impacts of biogas production at an organic dairy farm for two modelled scenarios: (1) harvesting and ensiling of cover crops and cereal straw and co-digestion with cattle manure, or (2) mono-digestion of cattle manure and direct cover crop soil incorporation. The biogas scenarios were modelled in a consequential LCA in relation to a common baseline without anaerobic digestion, with cover crop soil incorporation and field application of raw cattle manure. Biogas scenarios resulted in decreased global warming impacts of (1) 250 and (2) 120 Mg CO2eq for a 1000-hectare example dairy farm due to substitution of natural gas. However, emissions from ensiling, biogas plant operation, and agronomic effects increased other environmental impacts. Agronomic modelling with the Daisy model showed a crop yield increase of 0.11 Mg DM ha−1 year−1 on a sandy loam soil with cover crop digestion, but also an increase in N leaching of 38% and a decrease in soil C stocks of 8.1 Mg C ha−1 over 100 years relative to the reference. Emissions of VOCs and NOx during ensiling increased ozone formation and negative impacts on human health and ecosystems, although further research is needed to better understand these emissions. In conclusion, this modelling study shows that greenhouse gas emissions can be reduced by using ensiled cover crops for co-digestion with manure when biogas is used to substitute fossil gas, although trade-offs with other environmental categories must be considered.