The biological composition of the material exported to a moored sediment trap located under the winter mixed layer of the naturally fertilized Kerguelen Plateau in the Southern Ocean was studied over an annual cycle. Despite iron availability in spring, the annual particulate organic carbon (POC) export (98.2 mmol m−2) at 289 m was low, but annual biogenic silica export was significant (114 mmol m−2). This feature was related to the abundance of empty diatom cells and the ratio of full to empty cells exerted a first-order control in BSi : POC export stoichiometry of the biological pump. Chaetoceros Hyalochaete spp. and Thalassiosira antarctica resting spores were responsible for more than 60% of the annual POC flux that occurred during two very short export events of < 14 days in spring–summer. Relatively low diatom fluxes were observed over the remainder of the year. Faecal pellet contribution to annual carbon flux was lower (34%) and reached its seasonal maximum in autumn and winter (> 80%). The seasonal progression of faecal pellet types revealed a clear transition from small spherical shapes (small copepods) in spring, to larger cylindrical and ellipsoid shapes in summer (euphausiids and large copepods) and finally to large tabular shapes (salps) in autumn and winter. We propose in this high-biomass, low-export (HBLE) environment that small but highly silicified and fast-sinking resting spores are able to bypass the intense grazing pressure and efficient carbon transfer to higher trophic levels that are responsible for the low fluxes observed the during the remainder of the year. More generally our study also provides a statistical framework linking the ecological succession of diatom and zooplankton communities to the seasonality of carbon and silicon export within an iron-fertilized bloom region in the Southern Ocean.