Agroforestry is often mentioned as a suitable technology for land rehabilitation in the tropics and for mitigation of climate change because this land-use favours nutrient recycling and C sequestration. The aim of this work was to estimate soil C sequestration in a 12-year-old tropical silvopastoral system composed of a legume tree (Gliricidia sepium) and a C4 fodder grass (Dichanthium aristatum), and to link it with tree root biomass and N status in the soil. The site was under cut-and-carry management, i.e. tree pruning residues and cut grass were removed from the field and fed to stabled animals elsewhere. Thus, main sources for tree C and N inputs were root activity and turnover. Organic C derived from the trees and tree root biomass were determined based on natural ¹³C abundance. For the 0–0.2 m soil layer, the biomass of tree roots ≤2 mm diameter was 2.4 Mg/ha when the trees were pruned every 6 months (SS6), and 0.6 Mg/ha when pruned every 2 months (SS2). Both C (R² = 0.39, P < 0.05) and N (R² = 0.82, P < 0.05) sequestration were correlated with tree root biomass. The trees and grass contributed 18 and 8 Mg C/ha to soil, respectively, over the 12-year experiment in SS6. The net increase of 2.5 Mg N/ha in soil, originating from the trees, contributed to the net soil C sequestration. In SS2, trees contributed 16 Mg C/ha to soil over 12 years, but grass-derived C was reduced by 2 Mg C/ha because of the small amount of grass litter. The increase of 1.7 Mg N/ha in soil, derived from the trees, was not large enough to avoid C loss in this plot. Differences in soil C and N sequestration between plots were due to differences in system management, which affected the amount and the C/N ratio of inputs and outputs.