Perennial C4 bioenergy crops can combine high productivity and low input requirements. However, their impact on soil organic carbon (SOC) stocks remains uncertain. The aim of this study was to assess the long-term impact of converting arable land to perennial bioenergy crops on SOC stocks for two crop species (miscanthus and switchgrass) and several crop management practices (nitrogen fertilization, harvest date and irrigation). We analyzed two long-term experiments. Site 1 was located in Estrées-Mons, northern France (49.872°N, 3.013°E), and corresponded to the INRAE long-term experiment called “Biomass & Environment”. Site 2 was located in Montgaillard-Lauragais, southern France (43.433°N, 1.679°E), and was managed by Arvalis. Both sites were sampled initially and after 12 (site 1) or 13 (site 2) years. SOC concentrations, δ13C values and bulk densities were measured in order do calculate SOC stocks at equivalent soil mass and changes in “new” and “old” SOC stocks. The dataset is organised to calculate stocks at equivalent soil mass using the SimpleESM R script (https://github.com/fabienferchaud/SimpleESM).