The production of organic carbon in the ocean’s surface and its subsequent downward export transfers carbon dioxide to the deep ocean. This CO2 drawdown is countered by the biological precipitation of carbonate, followed by sinking of particulate inorganic carbon, which is a source of carbon dioxide to the surface ocean, and hence the atmosphere over 100–1,000 year timescales1. The net transfer of CO2 to the deep ocean is therefore dependent on the relative amount of organic and inorganic carbon in sinking particles2. In the Southern Ocean, iron fertilization has been shown to increase the export of organic carbon3,4,5, but it is unclear to what degree this effect is compensated by the export of inorganic carbon. Here we assess the composition of sinking particles collected from sediment traps located in the Polar Frontal Zone of the Southern Ocean. We find that in high-nutrient, low-chlorophyll regions that are characterized by naturally high iron concentrations, fluxes of both organic and inorganic carbon are higher than in regions with no iron fertilization. However, the excess flux of inorganic carbon is greater than that of organic carbon. We estimate that the production and flux of carbonate in naturally iron-fertilized waters reduces the overall amount of CO2 transferred to the deep ocean by 6–32%, compared to 1–4% at the non-fertilized site. We suggest that an increased export of organic carbon, stimulated by iron availability in the glacial sub-Antarctic oceans, may have been accompanied by a strengthened carbonate counter pump.