The dataset contains 361 records of energy density values measured on (eviscerated) whole bodies of meso- to bathypelagic fish (49 species), decapods (4 species) and euphausiids (1 species), collected in the Bay of Biscay (temperate Atlantic) and in the tropical Atlantic. 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. Samples from the tropical Atlantic were collected during the MAFIA Cruise (29HE20150403) carried out on the R/V Hespérides in April 2015 (López-Pérez et al. 2023). In both cases, energy density was measured directly by bomb calorimetry methods on dried homogenized samples, as described in detail in Spitz et al. (2010) and López-Pérez et al. (2023). Energy density values are presented as a function of both dry and wet mass, and the moisture percentage of samples is also given.