Context There is little information on the effects of tree densities and ages of silvopastoral systems (SSPs) on total soil carbon stock (TSCS). Aims This study aimed to evaluate the TSCS, carbon and nitrogen fractionation and biological activity in SSPs planted with Eucalyptus grandis in different densities and ages. Methods Two SSPs (333 or 166 trees ha−1) and one full sun pasture (FSP) grown for 5 or 7 years and native vegetation (NV) were evaluated (seven treatments). Samples were collected up to 1 m deep to evaluate the variables. Key results Particulate organic carbon (POC) and particulate organic nitrogen (PON) were higher (P < 0.05) in FSP (14.1 and 0.725 g kg−1), intermediate in SSP (9.88 and 0.46 g kg−1) and lower in NV (6.12 and 0.29 g kg−1). TSCS was 44.8% (194 vs 134 Mg ha−1; P < 0.001) higher in SSP and FSP compared to NV. Higher tree density reduced TSCS in younger systems, but without effect on older systems. TSCS was 13.7% (207 vs 182 Mg ha−1; P = 0.026), POC was 52.0% (11.9 vs 7.83 g kg−1; P < 0.001) and PON was 54.4% (0.556 vs 0.360 g kg−1; P < 0.001) higher in SSP for 7 compared to 5 years, respectively. Conclusions Tree density had a limited effect on TSCS. Higher SSP age increased carbon sequestration, probably due to greater cycling in the particulate fraction and better biological activity. Implications The SSP and well-managed FSP are good strategies to increase TSCS compared to NV, and their use can improve environmental indicators.