The oceans store a substantial fraction of carbon as calcium carbonate (CaCO3) and organic carbon (Corg) and constitute a significant component of the global carbon cycle. The Corg and CaCO3 flux depends on productivity and is strongly modulated by the Asian monsoon in the tropics. Anthropogenic activities are likely to influence the monsoon and thus it is imperative to understand its implications on carbon burial in the oceans. We have reconstructed multi-decadal CaCO3 and Corg burial changes and associated processes during the last 4.9 ky, including the Meghalayan Age, from the Gulf of Mannar. The influence of monsoon on carbon burial is reconstructed from the absolute abundance of planktic foraminifera and relative abundance of Globigerina bulloides. Both Corg and CaCO3 increased throughout the Meghalayan Age, except between 3.0–3.5 ka and the last millennium. The increase in Corg burial during the Meghalayan Age was observed throughout the eastern Arabian Sea. The concomitant decrease in the Corg to nitrogen ratio suggests increased contribution of marine organic matter. Although the upwelling was intense until 1.5 ka, the lack of a definite increasing trend suggests that the persistent increase in Corg and CaCO3 during the early Meghalayan Age was mainly driven by higher productivity during the winter season coupled with better preservation in the sediments. Both the intervals (3.0–3.5 ka and the last millennium) of nearly constant carbon burial coincide with a steady sea-level. The low carbon burial during the last millennium is attributed to the weaker-upwelling-induced lower productivity.