Agroforestry systems, i.e., agroecosystems combining trees with farming practices, are of particular interest as they combine the potential to increase biomass and soil carbon (C) storage while maintaining an agricultural production. However, most present knowledge on the impact of agroforestry systems on soil organic carbon (SOC) storage comes from tropical systems. This study was conducted in southern France, in an 18-year-old agroforestry plot, where hybrid walnuts (Juglans regia × nigra L.) are intercropped with durum wheat (Triticum turgidum L. subsp. durum), and in an adjacent agricultural control plot, where durum wheat is the sole crop. We quantified SOC stocks to 2.0 m depth and their spatial variability in relation to the distance to the trees and to the tree rows. The distribution of additional SOC storage in different soil particle-size fractions was also characterized. SOC accumulation rates between the agroforestry and the agricultural plots were 248 ± 31 kg C ha- 1 yr- 1 for an equivalent soil mass (ESM) of 4000 Mg ha- 1 (to 26–29 cm depth) and 350 ± 41 kg C ha- 1 yr- 1 for an ESM of 15,700 Mg ha- 1 (to 93–98 cm depth). SOC stocks were higher in the tree rows where herbaceous vegetation grew and where the soil was not tilled, but no effect of the distance to the trees (0 to 10 m) on SOC stocks was observed. Most of the additional SOC storage was found in coarse organic fractions (50–200 and 200–2000 µm), which may be rather labile fractions. All together our study demonstrated the potential of alley cropping agroforestry systems under Mediterranean conditions to store SOC, and questioned the stability of this storage.