•High sediment carbon burial in semi-enclosed mangrove habitat with high NPP.•Low carbon burial in aquaculture converted mangrove habitat.•Biological factors like litterfall and crab density act as primary controls.•Secondary controls were sediment accumulation rates and grain size. Tropical mangrove environments have high carbon sequestration potential and this ecosystem service is currently used in mitigating climate change. However, these environments are declining rapidly in developing countries, diminishing their carbon sequestration potential and may ultimately transforming them as carbon dioxide sources. This study investigated the carbon sequestration potential through sediment burial at three mangrove habitats of Cochin, South-West coast of India. High burial estimates were recorded at two mangrove stations (2.95 ± 0.79–10.41 ± 2.50 t C ha−1 yr−1), but consistent with other tropical mangrove areas. Lower burial rates were estimated at one station (0.57 ± 0.24 t C ha−1 yr−1). Eighty percent of the mangrove net primary productivity through litterfall (NPPL) was stored in the sediment at the station with the highest burial rate, which is demonstrative of a robust carbon sink. However, at a different site, which is subject to aquaculture, only 7.23 % of NPPL was buried in the sediment. A major portion of the fixed carbon at this site is presumably emitted back to the atmosphere or exported to adjacent water bodies. The median total regional mangrove carbon burial rate in this study was 2.95 t C ha−1 yr−1 and the organic carbon burial rate was 1.93 ± 0.75 t C ha−1 yr−1. Biological factors such as mangrove biomass, litterfall and crab density have played a major role in controlling the sediment carbon burial rate. Sediment texture and bulk sediment accumulation acted as secondary controlling factors. The carbon source characterisation in the sediment profile using stable isotope techniques revealed the organic carbon origin as mangrove litter. Gaining a better understanding of carbon sources, burial rates and their controlling factors in mangrove habitats aids in regional climate mitigation efforts and global efforts to increase the carbon sequestration potential of tropical mangrove systems.