Stratospheric ozone depletion and emission of greenhouse gases lead to a trend of the southern annular mode (SAM) toward its high-index polarity. The positive phase of the SAM is characterized by stronger than usual westerly winds that induce changes in the physical carbon transport. Changes in the natural carbon budget of the upper 100 m of the Southern Ocean in response to a positive SAM phase are explored with a coupled ecosystem-general circulation model and regression analysis. Previously overlooked processes that are important for the upper ocean carbon budget during a positive SAM period are identified, namely, export production and downward transport of carbon north of the polar front (PF) as large as the upwelling in the south. The limiting micronutrient iron is brought into the surface layer by upwelling and stimulates phytoplankton growth and export production but only in summer. This leads to a drawdown of carbon and less summertime outgassing (or more uptake) of natural CO2. In winter, biological mechanisms are inactive, and the surface ocean equilibrates with the atmosphere by releasing CO2. In the annual mean, the upper ocean region south of the PF loses more carbon by additional export production than by the release of CO2 into the atmosphere, highlighting the role of the biological carbon pump in response to a positive SAM event. Key Points The response of carbon fluxes varies between seasons More biological production at positive SAM south of 55S Uptake of natural CO2 in summer in contrast to mean response due to biology © 2013 The Authors. Global Biogeochemical Cycles published byWiley on behalf of the American Geophysical Union. © 2013 The Authors. Global Biogeochemical Cycles published byWiley on behalf of the American Geophysical Union.