In the modern era, rapid anthropogenic activities in the vicinity of the Himalayas disturb the carbon sequestration potential resulting in climate change. For the first time, this study estimates the biomass and carbon storage potential of Northeast India’s diverse land uses through a biomass estimation model developed for this region. The mean tree density in tropical, subtropical, and temperate forests was 539, 554, and 638 trees ha−1, respectively. The mean vegetation carbon stock was the highest for temperate forests (122.09 Mg C ha−1), followed by subtropical plantations (115.45 Mg C ha−1), subtropical forests (106.01 Mg C ha−1), tropical forests (105.33 Mg C ha−1), tropical plantations (93.00 Mg C ha−1), and temperate plantations (50.10 Mg C ha−1). Among the forests, the mean soil organic carbon (SOC) stock up to 45 cm depth was the highest for tropical forests (72.54 Mg C ha−1), followed by temperate forests (63.4 Mg C ha−1) and subtropical forests (42.58 Mg C ha−1). A strong relationship between the tree basal area and biomass carbon storage was found for all land-use types. The land-use transformation from agriculture to agroforestry, and grassland to plantations increased both vegetation carbon (VC) and SOC stocks. The corresponding increase in VC and SOC was 40.80 and 43.34 Mg C ha−1, respectively, in the former, and 83.18 and 97.64 Mg C ha−1 in the latter. In general, the landscape-level estimates were drawn from site-level estimates in a given land-use type, and therefore, the corresponding values might be overestimated. Nevertheless, the results provide baseline information on carbon stock which may serve as a reference for devising appropriate land-use change policies in the region.