The concentration of atmospheric carbon dioxide (CO2) is a crucial climate parameter as it has far-reaching implications on global temperature. The oceans are a significant sink for CO2. Biologically mediated carbon sequestration, in the form of both inorganic (CaCO3) and organic carbon (Corg), and its subsequent burial in marine sediments play a vital role in regulating atmospheric CO2. Understanding the distribution of carbon in marine sediments under different environments can help predict the fate of excess CO2 in the future. We studied the factors affecting the basin scale variation in carbon burial in the climatically sensitive northeast Indian Ocean, by using the data [CaCO3, Corg, Corg/Nitrogen, and isotopic ratio (δ13C, δ15N) of organic carbon] from a total of 718 surface sediments. The entire continental shelf and slope contain <10 % CaCO3. The highest CaCO3 is in the deepest parts of the central northeast Indian Ocean, away from the mouth of major river systems. Despite of the high productivity, the low Corg on the continental shelf is attributed to the well-oxygenated coarse-grained sediments. The lowest Corg is found in the well-oxygenated deeper central northeast Indian Ocean. Interestingly, the highest total carbon is in the deeper central and equatorial regions, far away from the highly productive marginal marine regions. Our study reveals that the grain size, terrigenous dilution, dissolved oxygen, and water masses strongly influence carbon accumulation in the northeast Indian Ocean, with only secondary influence of the productivity.