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.