Quantitative data on diet composition is key to understand prey–predator interactions and to parameterize ecosystem models. We compiled estimates of diet proportions from 26 mesopelagic fish species belonging to the families Myctophidae, Sternoptychidae and Gonostomatidae sampled in the central and Northeast Atlantic and Mediterranean Sea between 2009 and 2015. The dataset consists of the proportional contribution (mean ± standard deviation) of each food item (recorded to the lowest possible taxonomic resolution) to the diet of a sample of consumers, estimated from Bayesian stable isotope mixing models. For each data record, we also provided the sampling location, geographic coordinates, month and year of sample collection, method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, type of analyses and estimation method, as well as the reference and DOI of the original data source, for further details on the samples analysed and/or the analytical techniques used.