In the Ross Sea, biodiversity organisation is strongly influenced by sea-ice cover, which is characterised by marked spatio-temporal variations. Expected changes in seasonal sea-ice dynamics will be reflected in food web architecture, providing a unique opportunity to study effects of climate change. Based on individual stable isotope analyses and the high taxonomic resolution of sampled specimens, we described benthic food webs in contrasting conditions of seasonal sea-ice persistence (early vs. late sea-ice break up) in medium-depth waters in Terra Nova Bay (Ross Sea). The architecture of biodiversity was reshaped by the pulsed input of sympagic food sources following sea-ice break up, with food web simplification, decreased intraguild predation, potential disturbance propagation and increased vulnerability to biodiversity loss. Following our approach, it was possible to describe in unprecedented detail the complex structure of biodiverse communities, emphasising the role of sympagic inputs, regulated by sea-ice dynamics, in structuring Antarctic medium-depth benthic food webs.