Natural iron fertilization downstream of Southern Ocean island plateaus supports large phytoplankton blooms and promotes carbon export from the mixed layer. In addition to sequestering atmospheric CO2, the biological carbon pump also supplies organic matter (OM) to deep-ocean ecosystems. Although the total flux of OM arriving at the seafloor sets the energy input to the system, the chemical nature of OM is also of significance. However, a quantitative framework linking ecological flux vectors to OM composition is currently lacking. In the present study we report the lipid composition of export fluxes collected by five moored sediment traps deployed in contrasting productivity regimes of Southern Ocean island systems (Kerguelen, Crozet and South Georgia) and compile them with quantitative data on diatom and faecal pellet fluxes. At the three naturally iron-fertilized sites, the relative contribution of labile lipids (mono- and polyunsaturated fatty acids, unsaturated fatty alcohols) is 2–4 times higher than at low productivity sites. There is a strong attenuation of labile components as a function of depth, irrespective of productivity. The three island systems also display regional characteristics in lipid export. An enrichment of zooplankton dietary sterols, such as C27Δ5, at South Georgia is consistent with high zooplankton and krill biomass in the region and the importance of faecal pellets to particulate organic carbon (POC) flux. There is a strong association of diatom resting spore fluxes that dominate productive flux regimes with energy-rich unsaturated fatty acids. At the Kerguelen Plateau we provide a statistical framework to link seasonal variation in ecological flux vectors and lipid composition over a complete annual cycle. Our analyses demonstrate that ecological processes in the upper ocean, e.g. resting spore formation and grazing, not only impact the magnitude and stoichiometry of the Southern Ocean biological pump, but also regulate the composition of exported OM and the nature of pelagic–benthic coupling.