It has been reported that the large cardamom-based traditional agroforestry systems in the Darjeeling Himalaya of West Bengal, India represents a sustainable land use system with a high potential to store and sequester biomass carbon. Therefore, the present study was undertaken to evaluate the changes in biomass stock and carbon accumulation of this indigenous system along an altitudinal gradient. The study area was classified into three altitude classes as low (700–1200 m asl), mid (1200–1700 m asl) and high (> 1700 m asl). The biomass and carbon storage for low-, mid- and high-altitude classes was estimated at 630.17 and 296.18 Mg ha− 1, 397.05 and 186.61 Mg ha− 1 and 315.78 and 148.42 Mg ha− 1, respectively. Schima wallichi, Cryptomeria japonica and Cupressus cashmeriana were the most dominant species in the low-, mid-, and high altitudinal classes, respectively. The IVI and total biomass of the five dominant species in low-, mid- and high altitudes ranged from 17.34–26.04, 18.15–37.56, 27.13–42.43 and 9.05-133.75 Mgha− 1, 1.38–37.43 Mgha− 1 and 19.0-72.1 Mgha− 1 respectively. Schima wallichi occurred in all the altitudinal classes among the top five dominant species. Across all the altitudinal gradients, the average ecosystem carbon storage was estimated at 295.02 Mg ha− 1. The contribution of SOC to the ecosystem carbon stock increased with the increasing altitude. In contrast, the contribution of biomass carbon to the ecosystem carbon stock decreased with the increase in altitude. The ecosystem carbon stock estimated for the low-altitude class was 36.43% and 45.30% higher than the mid- and high-altitude agroforestry systems. The large cardamom-based agroforestry systems in the Darjeeling Himalayas are thus a prospective carbon sink, both in vegetation and soil due to higher tree densities and natural resource conservation-based traditional farming practices.