Carbon export from the ocean surface to depth is an important component of the biological carbon pump, a key regulator of the world’s climate. The Antarctic Marginal Ice Zone accounts for 15% of Southern Ocean primary production, however, limited observations mean that the variability and drivers of primary production and its link to export are poorly constrained. Using a combination of gliders, biogeochemical argo floats and satellite observations, we show that sea-ice impacts both primary production and export through its influence on the upper ocean vertical density structure, light availability, and nutrient supply. Resultant changes in community composition, coupled with variations in vertical stratification, appear to be important determinants of carbon transfer to depth. The response of primary production and carbon export to sea-ice indicates that the biological carbon pump in this region is sensitive to ongoing climate change and predictions of reduced sea-ice cover in the future.