Next to iron (Fe), recent phytoplankton-enrichment experiments identified manganese (Mn) to (co-)limit Southern Ocean phytoplankton biomass and species composition. Since taxonomic diversity affects aggregation time and sinking rate, the efficiency of the biological carbon pump is directly affected by community structure. However, the impact of FeMn co-limitation on Antarctic primary production, community composition, and the subsequent export of carbon to depth requires more investigation. In situ samplings of 6 stations in the understudied southern Weddell Sea revealed that surface Fe and Mn concentrations, primary production, and carbon export rates were all low, suggesting a FeMn co-limited phytoplankton community. An Fe and Mn addition experiment examined how changes in the species composition drive the aggregation capability of a natural phytoplankton community. Primary production rates were highest when Fe and Mn were added together, due to an increased abundance of the colonial prymnesiophyte Phaeocystis antarctica. Although the community remained diatom dominated, the increase in Phaeocystis abundance led to highly carbon-enriched aggregates and a 4-fold increase in the carbon export potential compared to the control, whereas it only doubled in the Fe treatment. Based on the outcome of the FeMn-enrichment experiment, this region may suffer from FeMn co-limitation. As the Weddell Sea represents one of the most productive Antarctic marginal ice zones, our findings highlight that in response to greater Fe and Mn supply, changes in plankton community composition and primary production can have a disproportionally larger effect on the carbon export potential.