Land use systems play a vital role in the storage of soil total nitrogen (STN) and terrestrial carbon stocks and offset of the atmospheric CO2 concentration. In this study, we estimated the overall-ecosystem carbon stocks under different land cover types in some parts of Southwestern Nigeria, sub-Saharan Africa (SSA). Soil carbon and total nitrogen concentrations were measured at 0–10, 10–20 and 20–30 cm soil depths for four land covers (forests (FOR), plantations (TP), woodlands (WD) and croplands (CP)). The aboveground biomass carbon (Mg C ha−1) followed the order: FOR (118.19 Mg C ha−1) > TP (64.57 Mg C ha−1) > WD (31.09 Mg C ha−1) > CP (17.31 Mg C ha−1). Soil organic carbon (SOC) and STN concentration in all land uses decreased significantly (p < 0.05) with depth increment. Total SOC stock in 0–30 cm soil layer follows the order: FOR land use (93.62 Mg C ha−1) > TP (60.87 Mg C ha−1) > WD (55.21 Mg C ha−1) > CP (50.23 Mg C ha−1). The majority of carbon stocks in our study area were concentrated in the aboveground and soil carbon pool. Overall, the total carbon stock (TCS) of FOR was 163.67 Mg C ha−1, 152.86 Mg C ha−1 and 107.98 Mg C ha−1, respectively, greater than that of CP, WD and TP, respectively. This result indicated that forests stored larger amount of TCS compared to croplands and woodlands. As such, agroforestry, forest plantations and forestry should be given serious considerations as strategies to sequester carbon. Land use management practices and disturbance history are major factors impacting changes in carbon storage among land use systems. Improved knowledge of these and their spatial and temporal variability is very important in understanding the global change in soil carbon stocks and in enhancing human capacity to implement mitigation and adaptation strategies.