Excessive cultivation of maize (Zea mays L.) as a biogas substrate has fired debate about potential land‐use change effects of bioenergy cropping systems. Cup plant ( Silphium perfoliatum L.) is a perennial biogas crop that provides more environmental services than maize. This study investigated (i) how to replace maize with cup plant as a biogas substrate in a large‐scale biogas plant located in southwest Germany, and (ii) how to optimize the energy and material cycles of such a biogas plant given the new feedstock. The biogas plant produces 1000 m3 biogas per hour with plans for it to be combined with a large dairy farm (1000 dairy units). It was found that the substitution of maize with cup plant as a biogas substrate results in a methane yield reduction of 10% to 20% due to lower biomass yields. However, there exists a strong potential to increase both biomass yields and biogas substrate quality of cup plant by optimizing establishment procedures and better genotypes. Furthermore, cup plant provides food and shelter for open land animals, including birds and insects, and could hence be a suitable alternative to maize for large biogas plants, being more environmentally beneficial. Extracting proteins from cup‐plant biomass could also help replace soy with locally produced protein for feeding cattle. Hydrothermal carbonization is a promising tool for closing nutrient cycles and for extracting phosphate from digestate, but more research is needed before it can be put into practice. © 2020 The Authors. Biofuels, Bioproducts and Biorefining published by Society of Chemical Industry and John Wiley & Sons, Ltd.