To develop a more sustainable bio-based economy, an increasing amount of carbon for industrial applications and biofuel will be obtained from bioenergy crops. This may result in intensified land use and potential conflicts with other ecosystem services provided by soil, such as control of greenhouse gas emissions, carbon sequestration, and nutrient dynamics. A growing number of studies examine how bioenergy crops influence carbon and nitrogen cycling. Few studies, however, have combined such assessments with analysing both the immediate effects on the provisioning of soil ecosystem services as well as the legacy effects for subsequent crops in the rotation. Here, we present results from field and laboratory experiments on effects of a standard first-generation bioenergy crop (maize) and three different second-generation bioenergy crops (willow short rotation coppice (SRC), Miscanthus × giganteus, switchgrass) on key soil quality parameters: soil structure, organic matter, biodiversity and growth and disease susceptibility of a major follow-up crop, wheat (Triticum aestivum). We analysed a 6-year field experiment and show that willow SRC, Miscanthus, and maize maintained a high yield over this period. Soil quality parameters and legacy effects of Miscanthus and switchgrass were similar or performed worse than maize. In contrast, willow SRC enhanced soil organic carbon concentration (0–5 cm), soil fertility, and soil biodiversity in the upper soil layer when compared to maize. In a greenhouse experiment, wheat grown in willow soil had higher biomass production than when grown in maize or Miscanthus soil and exhibited no growth reduction in response to introduction of a soil-borne (Rhizoctonia solani) or a leaf pathogen (Mycosphaerella graminicola). We conclude that the choice of bioenergy crops can greatly influence provisioning of soil ecosystem services and legacy effects in soil. Our results imply that bioenergy crops with specific traits might even enhance ecosystem properties through positive legacy effects.