The precipitation and export of carbonate by pelagic calcifiers is a source of carbon dioxide (CO2) to the atmosphere over 100-1000 year timescales. The net transfer of atmospheric CO2 to the ocean interior is thus dependent on the rain ratio (organic carbon:inorganic carbon) of particle export. Iron (Fe) fertilisation of Southern Ocean HNLC waters increases organic carbon flux to the deep ocean. However, the response of planktonic calcifiers to Fe enrichment and their impact on carbon drawdown is unknown. Here we show from particle analysis of sediment trap samples that natural iron supply leads to excess fluxes of inorganic carbon larger than those of organic carbon. Foraminifers are the dominant component of inorganic carbon flux (34-49%). Resulting rain ratios are <1; a unique occurrence south of the Subantarctic Front. Conservative estimates indicate that the production and flux of carbonate reduces deep ocean CO2 storage by 6-32% in Fe-fertilized waters compared to 1-4% at a non-fertilized control site. Our data suggest any Fe-fertilized increases in Subantarctic organic carbon export may be accompanied by a strengthened carbonate counter pump.