Cup plant cultivation as feedstock for anaerobic digestion has become an emerging topic in European Agriculture. Although there is a gap in methane yields between cup plant and the benchmark crop silage maize, cup plant as a perennial crop provides several ecological advantages. Amongst others, studies have proven its potential for carbon sequestration. With the present study, we addressed the gap in knowledge about biomass partitioning above- and belowground as well as recycling of organic matter and nutrients for cup plant and compared the results to silage maize. Therefore, a 2 year field experiment was conducted under practical conditions on rather shallow soil conditions in a low mountain landscape in Western Germany. Relevant plant fractions like litterfall, yield biomass and stubbles were collected continuously and analyzed for their nutrient contents. Results show that the cup plant is characterized by more than 2000 kg ha− 1 a− 1 of pre-harvest losses with a high palatability. In sum, only 77% of the grown cup plant biomass can be harvested in contrast to 96% of silage maize. Thus, an intense, element-specific nutrient recycling takes place in cup plant whereas this is negligible in silage maize. Furthermore, clearly different, element-specific nutrient exports with yield were highlighted. In cup plant, exports were distinctly lower for nitrogen but several times higher for calcium compared to silage maize. Cup plant also showed 36% more roots with higher root masses particularly in the subsoil.Graphical abstract