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Caragana microphylla, a native perennial leguminous shrub, is widely used for desertification control in China’s Horqin Sandy Land. We investigated the effects of afforestation using C. microphylla in areas with fixed and active dunes on soil carbon (C) and nitrogen (N) storage in the soil total and light-fraction (LF) organic matter. Compared to the values in the control areas, soil organic carbon (SOC) storage to a depth of 100 cm increased by 88%, 74%, and 145% at 9, 15, and 31 years after shrub planting, respectively; the corresponding values were 68%, 61%, and 195% for total nitrogen (TN) storage, 109%, 199%, and 202% for LF organic carbon storage, and 203%, 337%, and 342% for LF nitrogen storage. The soil light-fraction (LF) organic matter contributed significantly to total SOC and TN storage, despite the low proportion of total soil mass accounted for by the LF dry matter. Thus, afforestation using C. microphylla was an effective way to sequester C and to restore degraded soils, but the process was slow; it would take more than 100 years to fully restore SOC storage in active dunes through afforestation with C. microphylla in the Horqin Sandy Land.