Paleoclimatic reconstructions have provided a unique data set to test the sensitivity of climate system to changes in atmospheric CO2 concentrations. However, the mechanisms behind glacial/interglacial (G/IG) variations in atmospheric CO2 concentrations observed in the Antarctic ice cores are still not fully understood. Here we present a new multiproxy data set of sea surface temperatures (SST), dust and iron supply, and marine export productivity, from the marine sediment core PS2489-2/ODP Site 1090 located in the subantarctic Atlantic, that allow us to evaluate various hypotheses on the role of the Southern Ocean (SO) in modulating atmospheric CO2 concentrations back to 1.1 Ma. We show that Antarctic atmospheric temperatures are closely linked to changes in SO surface temperatures over the last 800 ka and use this to synchronize the timescales of our marine and the European Project for Ice Coring in Antarctica (EPICA) Dome C (EDC) records. The close correlation observed between iron inputs and marine export production over the entire interval implies that the process of iron fertilization of marine biota has been a recurrent process operating in the subantarctic region over the G/IG cycles of the last 1.1 Ma. However, our data suggest that marine productivity can only explain a fraction of atmospheric CO2 changes (up to around 40–50 ppmv), occurring at glacial maxima in each glacial stage. In this sense, the good correlation of our SST record to the EDC temperature reconstruction suggests that the initial glacial CO2 decrease, as well as the change in the amplitude of the CO2 cycles observed around 400 ka, was most likely driven by physical processes, possibly related to changes in Antarctic sea ice extent, surface water stratification, and westerly winds position.