AbstractBioenergy crops are expected to provide biomass to replace fossil resources and reduce greenhouse gas emissions. In this context, changes in soil organic carbon (SOC) stocks are of primary importance. The aim of this study was to measure changes in SOC stocks in bioenergy cropping systems comparing perennial (Miscanthus × giganteus and switchgrass), semi‐perennial (fescue and alfalfa), and annual (sorghum and triticale) crops, all established after arable crops. The soil was sampled at the start of the experiment and 5 or 6 years later. SOC stocks were calculated at equivalent soil mass, and δ13C measurements were used to calculate changes in new and old SOC stocks. Crop residues found in soil at the time of SOC measurements represented 3.5–7.2 t C ha−1 under perennial crops vs. 0.1–0.6 t C ha−1 for the other crops. During the 5‐year period, SOC concentrations under perennial crops increased in the surface layer (0–5 cm) and slightly declined in the lower layers. Changes in δ13C showed that C inputs were mainly located in the 0–18 cm layer. In contrast, SOC concentrations increased over time under semi‐perennial crops throughout the old ploughed layer (ca. 0–33 cm). SOC stocks in the old ploughed layer increased significantly over time under semi‐perennials with a mean increase of 0.93 ± 0.28 t C ha−1 yr−1, whereas no change occurred under perennial or annual crops. New SOC accumulation was higher for semi‐perennial than for perennial crops (1.50 vs. 0.58 t C ha−1 yr−1, respectively), indicating that the SOC change was due to a variation in C input rather than a change in mineralization rate. Nitrogen fertilization rate had no significant effect on SOC stocks. This study highlights the interest of comparing SOC changes over time for various cropping systems.