Background: Tropical forests play a critical role in global biodiversity conservation and carbon storage. In human-modified landscapes, secondary forests are becoming increasingly common, yet their ecological functioning remains underexplored. Comparing the forest dynamics in mature and regenerating forests offers insights into forest recovery and carbon dynamics. Aims: To compare forest structure, floristic composition, stand dynamics and carbon of a mature and secondary tropical rainforest. Methods: We assessed tree community and carbon dynamics over 5 years in two 1-ha long-term ecosystem monitoring plots, one each in mature tropical rainforests (MR) and 10-year post-agroforestry secondary rainforests (SR) in India’s Western Ghats mountains. Both plots were established in 2017 and monitored annually. We expected (1) higher tree diversity, differences in species composition, and greater carbon stock in MR; (2) higher carbon sequestration rates in SR; and (3) carbon dynamics shaped by growth and mortality in SR and MR, respectively. Results: The SR plot had fewer species (67 vs. 84), stored substantially less carbon (76 vs. 193 Mg), and comprised a distinct community with fewer late-successional species than MR. SR gained 5.8 Mg carbon, due to tree growth exceeding losses from mortality, while in MR mortality exceeded growth and recruitment resulting in a 3.3 Mg carbon decline over five years. Conclusion: While MR had higher tree diversity, carbon stocks and relatively intact composition, the high rates of biodiversity and carbon accrual in SR highlight the conservation and climate significance of post-agroforestry secondary forests. Moderate carbon losses noted here in MR, as in other mature South Asian tropical forests, is a cause for concern under ongoing climate change.