Information is needed on how anomalous environmental conditions affect important Antarctic ecological sentinels during the winter. Using a non-invasive method (scats), the diet of non-breeding gentoo penguins Pygoscelis papua at Bird Island, South Georgia, was examined during the winter of 2009 when local environmental conditions were abnormal (e.g. warmer sea surface waters). Scats were collected every 2 weeks from May until October 2009 (N = 168); the diet was dominated by the amphipod Themisto gaudichaudii by frequency of occurrence (77.5% of the samples) and by number (70.5% of the total individuals). By mass, different species of crustaceans (T. gaudichaudii and Antarctic krill Euphausia superba) and fish (Champsocephalus gunnari, Lepidonotothen larseni and Pseudochaenichthys georgianus) were the most important in different periods. Numerically, prey switching occurred at the end of winter, when E. superba became more abundant in the penguins’ diets in late September and early October (austral spring), when sea surface temperatures became colder. T. gaudichaudii is sub-optimal prey for gentoo penguins and its consumption most likely reflects a lack of E. superba in local waters. The consumption of T. gaudichaudii and fish, in place of E. superba, was probably insufficient for the penguins to maintain a body condition suitable for reproduction, contributing to the observed late commencement of breeding (i.e. 2–3 weeks) that year. Our results highlight the sensitivity of gentoo penguin populations to variations in environmental conditions, particularly in terms of how these conditions affect the availability of preferred dietary items and potential follow-on effects in the subsequent breeding season.