In this study, we investigated the fatty acid composition of the non-feeding stage of barnacle larvae (cyprids) using an integrative (larvae–environment) and comparative (latitudinal) approach. We measured fatty acids in the pelagic particulate matter and cyprids from Chthamalus bisinuatus, C. proteus, and Semibalanus balanoides from tropical to polar (Arctic) latitudes to identify potential food sources during the feeding larval stages (nauplius) that precede the cyprids and to ascertain larval capacity to integrate neutral (energetic) and polar (structural) fatty acids. Here we provide the complete dataset of all fatty acids detected both in i) the total particulate matter (TPM) present in the water column, and ii) the cyprid larvae of the different barnacle species. This could be useful in comparing data with future studies investigating fatty acid trophic markers in nearshore habitats. Raw data of biophysical paramateres includes cyprid i) size, ii) supply and (iii) settlement, as well as temperature collected using waterproof loggers (HOBO Pendant® Temperature/Light 64K). Image provided corresponds to the cyprid of the acorn barnacle Semibalanus balanoides, showcasing multiple lipid droplets, ie., the cyprid's main lipid storage organelles that store fat in the form of neutral lipids.