Abstract Cover cropping is important for nutrient management of agricultural systems and has largely unexploited potential for biogas production. Co-harvest of cover crops and straw and storage as silage blends prior to biogas is promising as it could enhance the long-term storability and lead to synergies for anaerobic digestion. However, it is necessary to evaluate the feasibility of using co-ensiled blends and process optimization based on continuous test. In this study, semi-continuous thermophilic anaerobic digestion experiments were carried out with feeding of cover crop silage, co-ensiled cover crop and straw (with mixing ratios in relation to various harvest strategies) with or without addition of cattle manure. The main objective is to determine the feasibility of aforementioned mixtures for biogas production and the influence on microbial community structures in response to various feeding compositions. Results demonstrated that cover crop (silage) is feasible for digestion alone or with addition of barley straw, cattle manure or both, while manure addition led to higher CH4 yield/buffer capacity, and enhanced the volatile solids reduction. Microbial community compositions were found to have been affected by the feeding, while high straw addition led to a distinct community structure.