This dataset includes results from lipid analysis and fatty acid profiles of Calanidae collected during cruise M153 with RV Meteor (February 15 to March 28, 2019) and during cruise SO285 with RV Sonne (September 15 to October 7, 2021) with the same sampling scheme in the northern (nBUS) and southern (sBUS) Benguela Upwelling System. The cruises were part of the TRAFFIC (Trophic tRAnsfer eFFICiency in the Benguela Current) project. Samples were retrieved from vertical multinet Midi hauls (200 µm mesh size). The aim was to identify distribution patterns in relation to environmental conditions and the comparison of horizontal, vertical and trophic niches of close-related, similar-sized key species in the BUS.