The subduction and release of carbon at convergent margins is a primary mechanism by which tectonic processes influence atmospheric pCO2, but the balance between the amount of carbon subducting and the CO2 flux from volcanic arcs remains poorly constrained. Estimating CO2 recycling efficiency in complex regions like the Sunda margin, Indonesia, is particularly difficult due to the lateral variability in sediment thickness, composition, and fraction subducted. We present a new approach for estimating sedimentary carbon flux that combines high-precision carbon content and isotope measurements with a regional sediment and unit thickness model we generated from seismic profiles to more accurately extrapolate compositional measurements from sediment core sites to the margin. Our results suggest that the subducting sedimentary carbon flux is up to an order of magnitude less than previous estimates and cannot alone account for the volume of CO2 released along the volcanic arc. Together, this and the isotopic composition of subducting sedimentary carbon suggest that an additional isotopically heavy carbon source contributes to the released CO2. Carbon from carbonate—likely from subducted altered oceanic crust and the overriding plate—can account for the discrepancy between both amount and isotopic composition of sedimentary carbon influx and those of volcanic CO2 efflux. These results highlight the importance of considering the full range of subduction zone processes operating at individual margins in order to better understand the cycling of carbon and other elements. Similar scrutiny should be applied in the evaluation of carbon subduction inputs to other subduction margins to improve global estimates of tectonic carbon cycling.