The Galapagos sea lion, Zalophus wollebaeki (GSL), is endemic to the Galapagos Archipelago and is considered endangered by the International Union for Conservation of Nature (IUCN). Population status has undergone a drastic decline over the last four decades, partially due to oceanographic anomalies like El Niño-Southern Oscillation (ENSO) events. To assess the impact of the strong 2015–2016 ENSO on GSLs, their diet diversity, trophic niche breadth, and trophic level (TL) from 2014 to 2016, were evaluated through scat analysis (N = 360; 120 samples per year) in San Cristóbal Island. The overall trophic spectrum comprised 72 species, mainly fish species and one squid species; the most important prey (IIMP) during the study period were Opisthonema berlangai (11.51%), Vinciguerria lucetia (8.82%), and Symphurus spp. (8.17%). There were no significant interannual differences (F=2.15, p=0.104) in the abundance of prey from six different habitats; however, GSLs consumed a greater abundance (47%) of benthic prey in 2015. The PERMANOVA analysis detected interannual dietary differences (F=11.9, p=0.001) and the NMDS test indicated that, GSL consumed a greater proportion of benthic prey in 2015. The GSL can be classified as a specialist consumer (Bi=0.21), with the lowest value in 2015 (Bi=0.06). The overall TL was 4.6, indicating a secondary-tertiary consumer. The presence of prey from different habitats (benthic, epipelagic, reef, and mesopelagic) suggests a diversification strategy to reduce resource overlap between individuals. This apex predator exhibited trophic flexibility during ENSO, evidenced by a rapid response to anomalous environmental conditions that included reducing the foraging niche and increasing the consumption of prey from greater depths. These findings highlight the importance of this species as a bio-indicator for environmental changes around Galapagos Islands, a unique ecosystem that is a marginal habitat for this endangered species.