This file contains data on mesopelagic fish stomach content reported as the number of prey categories in each fish stomach and their carbon masses. These data come from samples collected around the Iberian Peninsula (sampled during the CSIC-SUMMER cruise in October 2020). 120 samples come from the western Mediterranean and 173 from the Atlantic. Overall 42 different prey taxa could be identified from the stomachs. Five zones around the Iberian Peninsula were studied: south of the Balearic Islands, Alboran Sea, Gulf of Cadiz, off Lisboa and off Galicia. The table contains 5785 prey data records from 293 stomachs of 29 species of mesopelagic fish. Each data record (row) corresponds to one prey item, therefore for each fish stomach there are as many records as number of prey in the stomach. The complete dataset presents predators (mesopelagic fish) identified to species level, and prey taxa identified to genus level when possible (42 prey taxa). The studied mesopelagic fish correspond to orders Stomiiformes and Myctophiphormes and were selected because they were the most common and abundant in the cruise. The most diverse group was Myctophidae, with 14 species. The Stomiiformes were represented by four families, of which 5 species were Gonostomatidae, 2 Phosichthyidae, 4 Sternoptychidae and 4 Stomiidae.