The Arctic Ocean faces a complete loss of the summer sea ice cover in the coming decades. Sea ice is an important habitat for microalgae ('ice algae') and a diverse ice-associated community. Hence, the rapid deterioration of sea ice habitats will cause major repercussions on the structure and functioning of Arctic ecosystems. How sea ice habitat structure shapes the ice-associated community, however, is barely understood. Using an under-ice trawl equipped with a bio-environmental sensor array throughout the Eurasian Basin, we investigated (1) the relationship between sea ice properties, and under-ice community structure; (2) the under-ice distribution of polar cod Boreogadus saida, an important carbon source for Arctic endotherms, and (3) the significance of ice algal carbon for a number of key species from the under-ice habitat. According to sea ice structure and other parameters, the environment was separated in two distinct regimes, which was resembled in the under-ice community structure. Polar cod were ubiquitous throughout the Eurasian Basin. Higher fish abundance was associated with thicker ice, higher ice coverage and lower surface salinity. Back-tracking of the ice floes hosting polar cod indicated potential areas of under-ice recruitment on the Siberian shelf. First results from fatty acid and stable isotope analysis indicate a significant contribution of ice algal carbon to the carbon budget of the food web at multiple trophic levels. This, in combination with the observed response in community composition to different environmental regimes indicates potential long-term alterations in Arctic marine ecosystems as the Arctic Ocean continues to change. Additionally, the omnipresence of polar cod in the Eurasian Basin indicates that the central Arctic under-ice habitats may constitute a potential vector of genetic exchange and a recruitment source for coastal populations around the Arctic Ocean.