Deforestation and forest degradation can impact carbon dynamics and, subsequently, ecosystem functioning and climate change. In this study, we surveyed the influence of such land cover changes on four land cover/uses including closed canopy forest, tree fallow, shrub fallow, and degraded land among 120 study sites. We assessed these changes on total carbon stocks including both aboveground biomass (AGB) and soil organic carbon (SOC) including both topsoil, 0–30cm, and deep soil, 30–100cm. The four land cover/uses were located within four regions (Andasibe, Didy, Anjahamana, and Lakato) in the Eastern humid tropical forest of Madagascar. Our results show that total carbon stocks, AGB and soil, average 166±57MgCha−1 in which 82% is stored in 0–100cm of soil surface horizon (55% stored in the topsoil and 27% in deep soil) suggesting the importance of soil pools in the sequestration of atmospheric carbon. The total carbon stocks were significantly higher in closed canopy compared to the other land covers. In lower altitude regions, the total carbon stock was lower ranging from 143.5MgCha−1 to 163.7MgCha−1, relative to higher altitude areas where total C stock ranged from 170.6MgCha−1 to 186.1MgCha−1. The relative importance of AGB and SOC were reversed in these study sites, with AGB/SOC ratios of 0.37 for Anjahamana, 0.17 for Lakato, 0.21 for Didy, and 0.17 for Andasibe. Climatic factor combined with soil properties could explain the SOC variations across the study regions. High SOC was related to lower precipitation, high clay content and high root development. These results provide an accurate assessment of carbon storage distribution in a tropical region and support the importance of forest conservation and effective land cover management in maintaining carbon storage in ecosystems as tools in climate change mitigation in tropical forests.