The dataset contains 108 records of major and trace element concentrations measured on (eviscerated) whole bodies of meso- to bathypelagic fish (19 species), decapods (4 species) and euphausiids (1 species) collected around the Iberian Peninsula (temperate Atlantic and western Mediterranean), in the Bay of Biscay (temperate Atlantic), and in waters south of Iceland and in southern Irminger Sea (subarctic Atlantic). Samples around the Iberian Peninsula were collected on the CSIC-SUMMER cruise in October 2020 on R/V Sarmiento de Gamboa (Olivar et al. 2022). Samples from the Bay of Biscay were collected in autumn from 2002 to 2019, during the EVHOE fishery survey ("Evaluation Halieutique de l'Ouest de l'Europe"; https://doi.org/10.18142/8) conducted each year by the "Institut Français de Recherche pour l'Exploitation de la Mer" (Ifremer) on R/V Thalassa. Finally, samples from the subarctic Atlantic were collected in July 2020 during the IESSNS survey, icelandic part, on R/V (Ólafsdóttir and Pampoulie, 2021). For elemental analyses, aliquots of samples (~200 mg dry weight of homogenised specimens) were digested using a mixture of nitric and hydrochloric acids. Acidic digestion of the samples was performed overnight at room temperature and then in a microwave oven. Total concentrations of the micro-mineral phosphorus (P) and of the trace elements arsenic (As), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), selenium (Se) and zinc (Zn) were determined by inductively coupled plasma atomic emission spectrometry (ICP-OES) and/or mass spectrometry (ICP-MS). Total mercury (Hg) concentrations were also determined on aliquots of homogenised powder (50 ± 5 mg), by atomic absorption spectrophotometry using an Advanced Mercury Analyser. The quality assurance of these elemental analyses relied on blank and internal standard controls, and on the accuracy and reproducibility of data relative to the certified reference materials (CRMs) used in each analytical run. All elemental concentrations are given on a dry weight basis and can be converted on a wet weight basis according to the average percentages of moisture provided for each sample.