Sea-air exchange of carbon dioxide in the Southern Ocean is strongly seasonal, with ocean uptake in summer, which is partly offset by carbon dioxide outgassing in winter. This seasonal balance can shift due to sea ice conditions, inducing interannual variability in the Southern Ocean carbon sink. A decade (2010–2020) of unique, year-round marine carbonate chemistry observations from the Rothera Time Series (West Antarctic Peninsula) reveals that interannual variability in seawater fugacity of carbon dioxide depends on wintertime processes. Sea ice duration controls ocean stratification, which acts as a gateway to the carbon-rich ocean interior. Consequently, years with persistent sea ice cover and high mean winter stratification absorb, on average, 20% more carbon dioxide than years with less sea ice and weaker stratification in winter. Wintertime marine observations are therefore essential to resolve critical processes and reliably quantify interannual variability of the sea-air carbon dioxide flux in seasonally sea ice-covered regions. (Figure presented.)