Long-term dynamics of free living soil nematodes are driven by shifts in dominance structure not by colonization of new taxa. Cropping of Silphium perfoliatum L. fosters the fungal decomposer channel. Mass occurrences of Helicotylenchus spp. develop in cup plant stands of 9–10 years. Considering the landscape context soils in bioenergy production could benefit from cropping of S. perfoliatum. Positive effects on soil functions are expected for conversion of annual biomass crops to S. perfoliatum.