Over recent decades, a large uncultivated area has been converted to woodland and shrubland plantations to protect and restore riparian ecosystems in the Danjiangkou Reservoir area, a water source area of China's Middle Route of the South-to-North Water Transfer Project. Besides water quality, afforestation may alter soil organic carbon (SOC) dynamics and stock in terrestrial ecosystems, but its effects remain poorly quantified and understood. We investigated soil organic C and nitrogen (N) content, and delta C-13 and delta N-15 values of organic soil in plant root-spheres and open areas in an afforested, shrubland and adjacent cropped soil. Soil C and N recalcitrance indexes (RIC and RIN) were calculated as the ratio of unhydrolyzable C and N to total C and N. Afforestation significantly increased SOC levels in plant root-spheres with the largest accumulation of C in the afforested soil. Afforestation also increased belowground biomass. The C:N ratios in organic soil changed from low to high in the order the cropped, the shrubland and the afforested soil. The RIC in the afforested and shrubland were higher than that in cropped soil, but the RIN increased from the afforested to shrubland to cropped soil. The delta N-15 values of the organic soil was enriched from the afforested to shrubland to cropped soil, indicating an increased N loss from the cropped soil compared to afforested or shrubland soil. Changes in the delta C-13 ratio further revealed that the decay rate of C in the three land use types was the highest in the cropped soil. Afforestation increased the SOC stocks resulted from a combination of large C input from belowground and low C losses because of decreasing soil C decomposition. Shifts in vegetation due to land use change could alter both the quantity and quality of the soil C and thus, have potential effects on ecosystem function and recovery.