Changes in the world's oceans have altered nutrient flow, and affected the viability of predator populations when prey species become unavailable. These changes are integrated into the tissues of apex predators over space and time and can be quantified using stable isotopes in the inert feathers of historical and contemporary avian specimens. We measured δ13C and δ15N values in Flesh-footed Shearwaters (Puffinus carneipes) from Western and South Australia from 1936–2011. The Flesh-footed Shearwaters more than doubled their trophic niche (from 3.91 ± 1.37 ‰2 to 10.00 ± 1.79 ‰2), and dropped an entire trophic level in 75 years (predicted δ15N decreased from +16.9 ‰ to + 13.5 ‰, and δ13C from −16.9 ‰ to −17.9 ‰) – the largest change in δ15N yet reported in any marine bird, suggesting a relatively rapid shift in the composition of the Indian Ocean food web, or changes in baseline δ13C and δ15N values. A stronger El Niño-Southern Oscillation results in a weaker Leeuwin Current in Western Australia, and decreased Flesh-footed Shearwater δ13C and δ15N. Current climate forecasts predict this trend to continue, leading to increased oceanic ‘tropicalization' and potentially competition between Flesh-footed Shearwaters and more tropical sympatric species with expanding ranges. Flesh-footed Shearwater populations are declining, and current conservation measures aimed primarily at bycatch mitigation are not restoring populations. Widespread shifts in foraging, as shown here, may explain some of the reported decline. An improved understanding and ability to mitigate the impacts of global climactic changes is therefore critical to the long-term sustainability of this declining species.