Indigenous agroforestry systems are important reservoirs of biodiversity, and ecosystem services with a potential contribution for conservation of biodiversity while sustaining the livelihood of the rural populace. Pineapple (Ananas comosus) agroforestry systems (PAFS) form an essential constituent of the rural landscape in the Indian Eastern Himalayas and other parts of Asia. The traditional PAFS management in southern Assam is unique in that it involves shifting cultivation transitioning from native forests to a PAFS. Scarcity of information on the functioning and services in terms of species diversity and carbon storage potential in the traditional PAFS has restricted the opportunities for consideration under the nature-based solutions of climate action including REDD+. Therefore, the present study assessed the tree diversity and ecosystem carbon storage in a chronosequence from swidden agriculture through different phases of PAFS establishment. The result demonstrated that basal area in the PAFS increased with age. The most dominant species in the native forests was Palaquium polyanthum, while agricultural land use and PAFS aged <5, 11–15 and > 15 years old were dominated by Gmelina arborea, Albizia procera, Areca catechu and Hevea brasiliensis, respectively. The highest value of Shannon-Wiener diversity index (H) was recorded in native forests (2.71), and lowest in 5–10 years old PAFS. The ecosystem carbon storage declined from 261.43 Mg ha−1 in native forests to 181.07 Mg ha−1 in <5-years old PAFS. In <5 years old PAFS, the ecosystem carbon storage was 30 % lower than the native forest; while at >15 years it was merely 5 % less than the native forests. The traditional PAFS maintains a steady ecosystem carbon stock while reducing land use related carbon emission and providing additional co-benefits to the communities. Therefore, the traditional PAFS constitute a good opportunity for REDD+.