Ice retreat in West Antarctica and Antarctic Peninsula has led to important changes in seafloor communities and gains in benthic blue carbon. In most of the Antarctic, however, sea ice increased between the 1970s and 2014, but its effects on the benthos remain largely unexplored. Here, we provide a 1988–2014 record of macro- and megafauna from the north-eastern Weddell Sea shelf, where benthic biomass decreased by two thirds and composition shifted from suspension feeders to deposit feeders. Concomitant increases in sea-ice cover suggest a reduced flux of primary production to the benthos. As benthic communities are major repositories for Antarctic biodiversity and play an important role in biogeochemical cycling, the observed changes have far-reaching consequences for the Antarctic ecosystem and its feedback to the climate system. The findings underscore the importance of long-term ecological monitoring in a region vulnerable to warming and ice-shelf collapse