In deep-pelagic ecosystems, the trophic ecology of micronektonic species (such as fish, jellyfish, krill, shrimps, and cephalopods) is largely overlooked, with most research focusing almost exclusively on fish. However, like fish, invertebrate organisms play key roles in food webs, both as consumers and as predators. Here, we aimed to provide an integrated overview of the relative trophic position, segregation, and overlap of all main groups of species constituting the deep-pelagic micronektonic community. Stable nitrogen (δ15N) and carbon (δ13C) isotope compositions have thus been measured in 13 species belonging to three groups (jellyfish, crustaceans, and cephalopods) sampled in the Bay of Biscay slope area (Northeast Atlantic), as proxies for trophic level and feeding habitat of species. The addition of published isotopic data from deep-pelagic fish sampled in the same zone also allowed the inclusion of vertebrates in the analyses of the trophic structure of the community. The invertebrate community exhibited wide ranges of δ15N and δ13C values (6.45‰ and 2.71‰, respectively). Cephalopods appeared to segregate along a continuum of δ15N values, with important differences between muscular and fast-swimming species (Histioteuthis reversa and Todarodes sagittatus) presenting higher δ15N values than gelatinous species (Teuthowenia megalops and Haliphron atlanticus). In contrast, crustaceans appeared to have lower δ15N values and to be more strongly segregated by δ13C values, suggesting different feeding habitats (range δ13C = 2.71‰). Some species showed more pelagic (13C-depleted) signatures (e.g., Meganyctiphanes norvegica) while others showed 13C-enriched values, possibly corresponding to a more benthopelagic diet (e.g., the two Pasiphaeidae species). Isotopic niche calculations at the group level revealed important overlaps between cephalopods and fish, as well as between jellyfish and crustaceans. These results are of significant importance for understanding the complex functioning of growing interest deep-pelagic food webs on slope areas, by promoting a multi-taxa approach.