The large, 80-100 ppm, glacial-interglacial variations in atmospheric CO2 concentrations are today relatively well understood. However, low sediment accumulation in open ocean sediment cores generally prevents a fine, detailed comparison between marine and ice core records, in particular during ice ages. Core MD12-3394, retrieved from the Indian sector of the Southern Ocean, presents a very high sediment accumulation rate, which makes it possible to study in more details the climate-carbon cycle feedbacks during Marine Isotope Stage 3 (MIS 3) using a highly-resolved sedimentary archive. The thorium normalization method has been used to derive biogenic and lithogenic fluxes accounting for sediment focusing. Biogenic fluxes derived from XRF scanner measurements have been used as proxy for biological productivity. Temperature and atmospheric CO2 concentration reconstructions from the Vostok and EPICA Dome C Antarctic ice cores have been compared with the proxies derived from the sediment core. The results show an overall low lithogenic flux in this core, which can be explained by its isolation. The lithogenic flux was particularly low during warm periods, and higher during cold periods. It peaked during the coldest periods of MIS 3. The biogenic fluxes are almost at zero during cold periods, and increase drastically when the climate became warmer. The opposite behavior of lithogenic flux and biogenic fluxes during warming phases, reducing lithogenic flux and increasing biogenic fluxes, point to an increasing upwelling enhancing the biological productivity. These results show that increased upwelling that contributed to the deglacial rise of atmospheric CO2 was also active during the smaller-scale warming periods within the last ice age. This implies that the underlying mechanisms controlling the upwelling in the Southern Ocean, and by inference the transfer of previously sequestered CO2 to the atmosphere, are reactive on a submillennial scale.