Northeast India is rich in biodiversity; however, in recent decades due to increase in population and demand for economic development, this region has encountered massive changes in its land use. In this study, we analyzed the changes of carbon storage in Assam, Meghalaya, Manipur, Nagaland, and Tripura as a result of land-use conversion and land-use management between 2006 and 2013. Results indicated an increase in settlement areas and agricultural areas at the expense of forest areas and other land-use cover. However, the extent of various land uses varies from state to state. Whereas Assam, Manipur, and Tripura experienced a net accumulation of soil organic carbon (SOC) as a result of land-use conversion by an amount of approximately 3.91, 0.22, 0.13 TgC, SOC declined in Meghalaya and Nagaland by approximately 0.11 and 0.62 TgC, respectively. Assam, Manipur, Meghalaya, and Nagaland experienced net decreases in carbon biomass between 2006 and 2013 by approximately 0.43, 1.51, 0.31, and 0.49 TgC, respectively; however, Tripura experienced a net accumulation of carbon biomass by approximately 0.12 TgC. Fuel wood gathering from forest and grassland management in Northeast (NE) India resulted in significant amounts of carbon emissions. However, there is a regional difference in the amount of changes in carbon stock due to agricultural management. Our result highlights the paramount significance of proper land-use management in NE India in view of reducing carbon emission and in fighting against climate change.