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Forest's ecosystem is changing at an alarming rate and anthropogenic alteration of forests to other land use is a major driver of carbon (C) emission and biodiversity loss. We estimated ecosystem-level C stock and factors affecting C stock in six major forest types; tropical wet evergreen forest, montane subtropical forest, temperate forest, bamboo forest, quercus forest, and jhum land of the eastern Himalayan region (India). We determined ecosystem structure, biodiversity, and plant and soil C stock by laying random plots in each forest site. The average C stock was estimated in the range of 79.0–373.4 Mg C ha−1 and found significantly different among the forest types. Partitioning ecosystem C stocks in plant (24–55%), soils (43–75%), deadwood (1–4.8%) and litter (0.20–1.25%) components varied largely. Pearson correlation analysis shows a significant positive relation of basal area with species diversity, tree density, and ecosystem C stock. Linear mixed-effect model demonstrates the high influence of species density and soil moisture content on the ecosystem C stock. We recommend the inclusion of forest structural attributes and pedological characteristics while predicting synergies between C stock and future climatic conditions. Additionally, conversion of natural forests to jhum land should be minimized because they stored lesser ecosystem C stocks thus plays a minimum role in C accumulation and cycling. The study provides estimates of C stocks in major forests that can be useful in suggesting a path forward to partially fulfill India's commitments to REDD + policy. [Display omitted] • Determining ecosystem-level carbon stock is essential for carbon sink management. • Average carbon stock ranged from 79 Mg C ha−1 to 373 Mg C ha−1 in major forest types. • Tropical wet evergreen forests are major carbon sink in the eastern Himalayas. • Carbon stock is highly influenced by the stand density and soil moisture content. • Jhum forests practices should be reduced to enhance ecosystem carbon sink capacity. [ABSTRACT FROM AUTHOR]