The seabed of the Antarctic continental shelf hosts most of Antarctica's known species, including taxa considered indicative of vulnerable marine ecosystems (VMEs). Nonetheless, the potential impact of climatic and environmental change, including marine icescape transition, on Antarctic shelf zoobenthos, and their blue carbon-associated function, is still poorly characterised. To help narrow knowledge gaps, four continental shelf study areas, spanning a southern polar gradient, were investigated for zoobenthic (principally epi-faunal) carbon storage (a component of blue carbon), and potential environmental influences, employing a functional group approach. Zoobenthic carbon storage was highest at the two southernmost study areas (with a mean estimate of 41.6 versus 7.2 g C m−2) and, at each study area, increased with morphotaxa richness, overall faunal density, and VME indicator density. Functional group mean carbon content varied with study area, as did each group's percentage contribution to carbon storage and faunal density. Of the environmental variables explored, sea-ice cover and primary production, both likely to be strongly impacted by climate change, featured in variable subsets most highly correlating with assemblage and carbon storage (by functional groups) structures. The study findings can underpin biodiversity- and climate-considerate marine spatial planning and conservation measures in the Southern Ocean.