The aim of this study was to evaluate the potential of short rotation alley cropping systems (SRACS) to improve the soil fertility of marginal post-mining sites in Brandenburg, Germany. Therefore, we annually investigated the crop alleys (AC) and black locust hedgerows (ABL) of a SRACS field trail under initial soil conditions to identify the short-term effects of tree planting on the storage of soil organic carbon (SOC) and its degree of stabilization by density fractionation. We detected a significant increase in SOC and hot-water-extractable organic C (HWEOC) at ABL, which was mainly restricted to the uppermost soil layer (0–10 cm). After 6 years, the SOC and HWEOC accumulation rates at ABL were 0.6 Mg and 46 kg ha^?1 year^?1, which were higher than those in the AC. In addition, comparatively high stocks of approximately 4.6 Mg OC and 182 kg HWEOC ha^?1 were stored in the ABL litter layer. Density fractionation of the 0–3 cm soil layer at ABL revealed that the majority of the total SOC (47%) was stored in the free particulate organic matter fraction, which was more than twice that of the AC. At the same time, a higher and steadily increasing amount of SOC was stored in the occluded particulate organic matter fraction at ABL, which indicated a high efficiency for SOC stabilization. Overall, our findings support the suitability of black locust trees for increasing the soil fertility of the reclaimed mining substrate and, consequently, the high potential for SRACS to serve as an effective recultivation measure at marginal sites.