Antarctic biodiversity is affected by seasonal sea-ice dynamics driving basal resource availability. To (1) determine the role of intraspecific dietary variability in structuring benthic food webs sustaining Antarctic biodiversity, and (2) understand how food webs and the position of topologically central species vary with sea-ice cover, single benthic individuals’ diets were studied by isotopic analysis before sea-ice breakup and afterwards. Isotopic trophospecies (or Isotopic Trophic Units) were investigated and food webs reconstructed using Bayesian Mixing Models. As nodes, these webs used either ITUs regardless of their taxonomic membership (ITU-webs) or ITUs assigned to species (population-webs). Both were compared to taxonomic-webs based on taxa and their mean isotopic values. Higher resource availability after sea-ice breakup led to simpler community structure, with lower connectance and linkage density. Intra-population diet variability and compartmentalisation were crucial in determining community structure, showing population-webs to be more complex, stable and robust to biodiversity loss than taxonomic-webs. The core web, representing the minimal community ‘skeleton’ that expands opportunistically while maintaining web stability with changing resource availability, was also identified. Central nodes included the sea-urchin Sterechinus neumayeri and the bivalve Adamussium colbecki, whose diet is described in unprecedented detail. The core web, compartmentalisation and topologically central nodes represent crucial factors underlying Antarctica’s rich benthic food web persistence.