Organisms accumulate major and trace elements (including metals) directly from the external environment and/or indirectly through diet. As such, their elemental composition can help to infer dietary preferences, solve trophic links and/or inform quantitative dietary analysis primarily based on carbon and nitrogen stable isotopes or on fatty acids (Lahaye et al. 2005, Ramos and González-Solís 2012, Soto et al. 2016, Majdi et al. 2018). This dataset reports the total concentrations of 30 major and trace elements analysed in whole bodies or in the muscle tissue of 82 unique species or genera characteristic of meso- to bathypelagic waters (referred as “mesopelagic”) or living on the continental shelf (referred as “other”). The species encompass jellyfish, crustaceans, cephalopods, fish, and were collected in North Atlantic and Mediterranean areas between 1968 and 2018. When available, the sampling method/gear as well as the sampling depth are specified. For the element mercury (Hg), the concentration of organic forms (referred as methyl-Hg) is also given when available, as well the percentage of these organic forms (% methyl-Hg) relative to total Hg. A column specifies whether concentrations are expressed on a dry weight or wet weight basis (weight of the animal tissue after being dried or containing water, respectively). All element concentrations given on a wet weight basis can be converted on a dry weight basis (and vice-versa if necessary) according to the percentages of moisture given for each sample analysed (when available). Data were compiled from 27 published studies/papers for which DOI are indicated, for further details and information on the samples analysed and/or the analytical techniques used.