Oceanic and deep-sea ecosystems play a key role in the cycling and vertical transfer of matter and energy in oceans. Their pelagic communities act as major components sustaining higher trophic level predators. Despite their location far from direct anthropogenic sources, deep-sea organism contamination by persistent organic pollutants has been proven, especially in demersal and benthic species. However, deep pelagic species have been far less studied, without mentioning contaminants of emerging concern. To fill these gaps, we studied the occurrence of a large variety of hydrophobic organic contaminants including polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), various brominated flame retardants (BFRs), including polybrominated diphenyl ethers (PBDEs) and their replacement substances BTBPE (1,2-bis(2,4,6-tribromophenoxy)ethane) and DBDPE (decabromodiphenylethane), and finally per- and polyfluoroalkyl substances (PFASs) in crustaceans and fish species collected in the deep pelagic waters of the Bay of Biscay, northeast Atlantic. The results highlighted the global predominance of PCBs (detection frequencies and concentrations) in fish, with mean concentrations of 54.42 ± 28.57 ng g -1 dry weight (dw), followed by OCPs (21.73 ± 21.26 ng g -1 dw), PFASs (11.95 ± 9.58 ng g -1 dw) and PBDEs (mean of 1.50 ± 1.12 ng g -1 dw). The concentrations showed moderate intra-species variability (21–38%) but were highly variable among species (43–87%). Total lipid contents were also highly variable (from 4.3% ± 0.9% to 51% dw in crustaceans and from 6.1% ± 0.1% to 41.9% ± 9.6% dw for fish) and showed little correlation with lipophilic contaminant concentrations. Most of the chlorinated or brominated contaminants showed increasing concentrations with increasing δ15N values, while most PFASs showed inverse trends. Hexa/heptachlorinated PCBs, DDTs and BDE-209 were the predominant compounds among chlorinated and brominated contaminants, while long-chain perfluorocarboxylic acids (PFCAs) prevailed among PFASs in most species. The contaminant profiles and diagnostic ratios revealed species-specific metabolic capacities.