The aim of this study was to check the suitability of using fatty acids of vegetable origin as biomarkers of aquafeed consumption in fish that aggregate around off-shore fish farms, analysing their different accumulation patterns and their persistence in different tissues in juveniles of Liza aurata (Risso, A. 1810. Ichthyologie de Nice ou histoire naturelle des poissons du département des Alpes-Maritimes. Schoell, Paris. 344 pp.). Their natural diet was replaced by a commercial feed, followed by a return to the natural diet (wash-out period). The fatty acid profiles of flesh, liver, and brain were modified after 2 months of commercial feed consumption, while 2 months of the wash-out period were not sufficient to return to original values, the brain being particularly resilient in this respect. Histological examination of the liver showed no alterations of the lipid droplet distribution or fat content. The combined use of flesh and brain for fatty acid analysis can be recommended for tracking aquaculture waste intake in the form of lost pellets by wild fish.