The Southern Ocean, a region highly vulnerable to climate change, plays a vital role in regulating global nutrient cycles and atmospheric CO2 via the biological carbon pump. Diatoms, photosynthetically active plankton with dense opal skeletons, are key to this process as their exoskeletons are thought to enhance the transfer of particulate organic carbon to depth, positioning them as major vectors of carbon storage. Yet conflicting observations obscure the mechanistic link between diatoms, opal and particulate organic carbon fluxes, especially in the twilight zone where greatest flux losses occur. Here we present direct springtime flux measurements from different sectors of the subpolar Southern Ocean, demonstrating that across large areas of the subpolar twilight zone, carbon is efficiently transferred to depth, albeit not by diatoms. Rather, opal is retained near the surface ocean, indicating that processes such as diatom buoyancy regulation and grazer repackaging can negate ballast effects of diatoms’ skeletons. Our results highlight that the presence of diatoms in surface waters of the Southern Ocean’s largest biome does not guarantee their importance as vectors for efficient carbon transfer through the subpolar twilight zone. Climate change-driven shifts in phytoplankton community composition may affect biologically sequestered carbon pools less than currently predicted.