The vertical export of particulate organic carbon (POC) from the upper ocean is a critical determinant of the efficiency of the biological carbon pump, i.e., how the biological pump affects atmospheric CO2. This is particularly relevant in the Southern Ocean (SO), the world’s most important region controlling atmospheric CO2. At high latitudes, the biological pump tends to be very effective in transforming net primary production to POC export, while at more equatorial latitudes, this export efficiency is lower. Here, we use the regional SO model ROMS-BEC with 4 phytoplankton functional types to disentangle the controls on the spatial variability in export efficiency. Through a set of model experiments, in which we successively turn off relevant aspects such as the temperature dependence of ecosystem processes or differences across phytoplankton types in the routing of biomass losses, we show that the simulated variability in export efficiency can only be explained by accounting for latitudinal differences in ecosystem structure. Of particular importance is the relative importance of diatoms for total biomass. We also find a strong sensitivity of the air-sea CO2 flux between 30-50°S to changes in POC export, i.e., changes in the biological pump efficiency. Varying the routing of diatom biomass losses to POC, we find that in this area, any change in POC export results in a change in oceanic CO2 uptake which amounts to 50% of the simulated change in POC export on the decadal time scales considered here. The sensitivity of the air-sea CO2 flux to changes in POC export is smaller (~7%) at high SO latitudes, possibly resulting from a quick resupply of respired carbon with upwelling, making the air-sea CO2 flux less dependent on the magnitude of downward POC fluxes. Consequently, on decadal time scales, our findings imply that any change in phytoplankton community structure and hence POC production and export has major impacts on oceanic CO2 uptake in the subantarctic and on the carbon export efficiency across the SO.