Squids were collected during the research cruise SO285 on RV Sonne in the northern (nBUS) and southern (sBUS) Benguela Upwelling System between September 13 and October 9, 2021 in order to determine their trophic position and nutritional ecology. The cruise was part of the TRAFFIC (Trophic tRAnsfer eFFICiency in the Benguela Current) project. Samples were retrieved from 17 rectangular midwater trawl (RMT) net hauls at 11 stations in the nBUS (sampling range 88–600 m) and 17 RMT net hauls at 14 stations in the sBUS (sampling range 80–750 m). Furthermore, hooks and lines were used at 10 stations in the nBUS (ranging from 15 to 160 min per station, 2–6 rods) and 13 stations in the sBUS (ranging from 20 to 105 min per station, 1–6 rods) in the upper two meters of the water column. Dorsal mantle length (DML) of each specimen was measured to the nearest mm below. This data set contains the results of the fatty acid trophic marker analyses of squid mantle muscle and midgut gland (MGG) tissue of 84 specimens. A modified carnivory index after Bode et al. (2015) was determined and ranged from 0.55 to 0.92. Differences in fatty acid compositions displayed distinct clusters separating squid families and different prey taxa through principal component analyses.