Two different processes control changes in the current and future Southern Ocean carbon uptake. The increase of atmospheric CO2 leads to uptake of anthropogenic carbon. Anthropogenic changes of the atmospheric circulation, however, also change the “natural” carbon budget. The predominant climate mode in the southern hemisphere is the Southern Annular Mode (SAM). In recent decades, the SAM showed a trend toward its positive phase, characterized by stronger westerlies. This trend is related to a warming atmosphere and is predicted to continue in the future. We analyze the response of the Southern Ocean carbon fluxes to the SAM-related variability in a hindcast simulation of a non-eddy-resolving general circulation model coupled to an ecosystem model with two phytoplankton classes. During a positive SAM event, stronger westerlies lead to more Ekman pumping. More carbon- and nutrient-rich deep water is brought into the mixed layer south of the Polar front. This leads to more outgassing of natural carbon, in line with previous model studies. On the other hand, the anomalous silicate and iron inputs favor primary production by diatoms and cause an overall increase of net primary production in our model. Accordingly, the export of organic carbon via the soft-tissue pump is increased. Primary production is responsible for a significant drawdown of the entrained carbon and its immediate return to the subsurface ocean, thereby reducing the amount of carbon available for sea-air gas-exchange. South of the Polar Front, the drawdown of CO2 by increased export production has a larger effect on the surface carbon inventory than the outgassing of CO2, underlining the role of the biological carbon pump for the inter-annual varying carbon fluxes. North of the Polar Front, primary and export production are reduced. In total this leads to an enhanced natural CO2 outgassing of 0.09 Pg C yr-1 per unit of SAM index south of 30°S in line with previous studies.