Abstract Sediments were sampled and oxygen profiles of the water column were determined in the Indian Ocean off west and south Indonesia in order to obtain information on the production, transformation, and accumulation of organic matter (OM). The stable carbon isotope composition (δ 13 C org ) in combination with C/N ratios depicts the almost exclusively marine origin of sedimentary organic matter in the entire study area. Maximum concentrations of organic carbon (C org ) and nitrogen (N) of 3.0% and 0.31%, respectively, were observed in the northern Mentawai Basin and in the Savu and Lombok basins. Minimum δ 15 N values of 3.7‰ were measured in the northern Mentawai Basin, whereas they varied around 5.4‰ at stations outside this region. Minimum bottom water oxygen concentrations of 1.1 mL L −1 , corresponding to an oxygen saturation of 16.1%, indicate reduced ventilation of bottom water in the northern Mentawai Basin. This low bottom water oxygen reduces organic matter decomposition, which is demonstrated by the almost unaltered isotopic composition of nitrogen during early diagenesis. Maximum C org accumulation rates (CARs) were measured in the Lombok (10.4 g C m −2 yr −1 ) and northern Mentawai basins (5.2 g C m −2 yr −1 ). Upwelling-induced high productivity is responsible for the high CAR off East Java, Lombok, and Savu Basins, while a better OM preservation caused by reduced ventilation contributes to the high CAR observed in the northern Mentawai Basin. The interplay between primary production, remineralisation, and organic carbon burial determines the regional heterogeneity. CAR in the Indian Ocean upwelling region off Indonesia is lower than in the Peru and Chile upwellings, but in the same order of magnitude as in the Arabian Sea, the Benguela, and Gulf of California upwellings, and corresponds to 0.1–7.1% of the global ocean carbon burial. This demonstrates the relevance of the Indian Ocean margin off Indonesia for the global OM burial.