The stomach contents of juvenile Magellanic penguins, Spheniscus magellanicus, stranded along the Atlantic coast (21–23°S) during the extreme mortality event of 2008 were analysed. The isotopic profiles of this species and their prey in a wintering area are presented to identify trophic relationships and to evaluate whether the prey species recovered in the stomach contents were assimilated. The prey groups recorded were molluscs (cephalopods and gastropods), teleost fish, and, to a lesser extent, crustaceans (decapods and isopods). Cephalopods were the most representative prey, and Argonauta nodosa was the most abundant species. Plant remains and solid waste were atypical items found in the stomach contents. The nitrogen isotope (δ15N) values found in this study confirm the higher trophic position of the penguins (14.5‰) relative to their prey (11.7–12.3‰). The carbon isotope (δ13C) measurements of all species are characteristic of marine coastal environments (−18.7 to −16.8‰). A Bayesian approach applied to stable isotope mixing models showed that cephalopods are assimilated to a greater extent than fish. However, the poor nutritional condition of specimens that reach the Brazilian coast, especially at the northern limit of migration (~21°S), indicates that prey ingestion is not sufficient for the maintenance of body weight.