The relative contribution of chemosynthesis in heterotrophic fauna at seeps is known to be influenced by depth and by habitat. Using stable isotopes of carbon and nitrogen, we investigated macro- and megafaunal nutritional patterns in Norwegian margin cold seeps by comparing food webs both among habitats within a seep site and between different sites. The very active Håkon Mosby mud volcano (HMMV) is characterized by geochemical gradients, microbial activity and faunal zonation from the centre to the periphery. The Storegga Slide (600–900 m depth) has pockmarks with patchy less active seeps, and also shows concentric zonation of habitats but at much smaller spatial scale. The dominant carbon source for macrofaunal nutrition in both areas was chemosynthetically fixed and the bulk of organic carbon was derived from sulphur-oxidizing bacteria. In HMMV, food chains were clearly separated according to habitats, with significantly lighter δ13C signatures on microbial mats and adjacent sediment (−33.06 to −50.62‰) than in siboglinid fields (−19.83 to −35.03‰). Mixing model outputs revealed that the contribution of methane-derived carbon was small in siboglinid fields (0–17%) but significant (39–61%) in the microbial mats. Moreover, the variability of macrofauna signatures within this later habitat suggests the co-occurrence of two food chains, one based on primary production via methanotrophy and the other via sulphide oxidation. The length of the food chains also varied among habitats, with at least one more trophic level in the siboglinid fields located at the periphery of the volcano. Conversely, in Storrega pockmarks, faunal δ13C signatures did not vary among habitats but among species, although separate food chains seem to co-occur. The small size of the seepage areas and their lower fluxes compared to HMMV allow more background species to penetrate the seep area, increasing the range of δ15N and the trophic level number. Probably due to the higher flux of photosynthetic particulate organic carbon, the overall chemosynthesis-based carbon contribution in invertebrate nutrition was lower than that in HMMV.