During the 2011 WACS cruise of RV Pourquoi Pas ? (Olu 2011, https://doi.org/10.17600/11030010), biomass-dominant fauna was sampled in several cold seep sites of the Gulf of Guinea (Regab, Guinness, Baboon and Worm Hole pockmarks) as well as in the Congo River deep-sea fan (lobes A, C and D). Stable isotope ratios of carbon and nitrogen of 406 samples belonging to >20 taxa and sediments were measured. Samples were prepared for analysis at the UMR6197 BEEP (Biologie et Ecologie des Ecosystèmes marins Profonds, Ifremer, Centre de Bretagne, France; https://www.umr-beep.fr/). Analytical measurements were performed at Geotop’s light stable isotope geochemistry laboratory (UQAM, Montreal, Canada). This data was used for the analyses underlying the paper "Environmental parameters and biotic interactions influence food web structure in deep-sea cold seeps from the Gulf of Guinea", by Loïc N. MICHEL, Marie PORTAIL, Dominique A. COWART, Pen-Yuan HSING, Lucie PASTOR, Karine OLU & Jozée SARRAZIN. The dataset consists of two files: one containing the data itself, and one describing all used terms (measurements or metadata).