In the context of climate change, understanding the ecological processes controlling the functioning and the efficiency of the biological pump is of primary importance. Plankton community structure and species-specific properties are often invoked as likely to affect biogeochemistry and the export of organic and biogenic material to the ocean interior. Although a major player in this respect, diatoms are still viewed as a single functional type whose diversity is generally overlooked. Here we examine that question, building on the results achieved during the MOBYDICK expedition, which occurred in the vicinity of the Kerguelen Islands (Southern Ocean) in late summer, a time window corresponding to the demise of the annually recurrent phytoplankton blooms already known to be controlled by iron availability. The Si/C/N stoichiometry of the particulate matter was studied in conjunction with the different diatom community structures, their physiological states, as well as their species-specific carbon contents and silicification degrees. Our results show that diatoms outside the iron-fertilized plateau were more heavily silicified, due to the combined effects of both taxonomic composition of the resident community and a direct physiological response to iron stress, resulting in higher Si:C elemental ratios in diatoms as well as in the bulk particulate matter. Despite low silicic acid concentrations, large chains of weakly silicified Corethron inerme were able to grow in the upper mixed layer above the plateau, while in adjacent high nutrient low chlorophyll (HNLC) waters, communities were dominated by Fragilariopsis spp., Cylindrotheca closterium and the centric genera Actinocyclus/Thalassiosira spp. Depth was also an important factor shaping diatom communities, with the presence of a deep and inactive assemblage located within the pycnocline gradient, both on- and off-plateau, which likely resulted from the differential sinking and accumulation of species previously grown at the surface. In HNLC waters, below the mixed layer, detrital frustules of the heavily silicified species Fragilariopsis kerguelensis carried mostly Si, while above the plateau, Eucampia antarctica and Chaetoceros spp. (resting spores and vegetative stages) were efficient vectors of both Si and C to the deeper layers. Our study shows that the stoichiometry of the biological pump cannot be considered solely as a simple response to a single limiting factor (here iron) highlighting the importance of a species-centered approach in order to finely resolve biogeochemical fluxes and improve our understanding of the biological pump.