Perennial non-food energy crops are currently discussed as a more sustainable alternative to conventional energy crops like maize. As they can be cultivated on marginal soils, they reduce the risk of land use and food vs. fuel conflicts. In this study, we evaluated the perennial energy crop Sida hermaphrodita for its potential to be cultivated on marginal substrate and conventional agricultural soils over a three-year field and mesocosm experiment at agricultural conditions. Furthermore, we aimed for a closed nutrient loop by fertilizing plants with biogas digestate and using the carbon fraction of the digestate as soil amendment to ameliorate the overall soil fertility. As controls, plants were either untreated or fertilized with an equivalent amount of mineral NPK fertilizer. We found S. hermaphrodita to give highest DM yields of up to 28 t ha(-1) under favorable soil conditions when fertilized with mineral NPK. However, on marginal substrate digestate fertilization resulted in a clear biomass yield advantage over NPK fertilization. An increased soil carbon content, water holding capacity and basal soil respiration indicated improved soil fertility in the marginal substrate. These results demonstrate the great potential of S. hermaphrodita to be cultivated on marginal soil in combination with organic fertilization via biogas digestate.