Cross-ecosystem nutrient subsidies play a key role in the structure and dynamics of recipient communities, but human activities are disrupting these links. Because nutrient subsidies may also enhance community stability, the effects of losing these inputs may be exacerbated in the face of increasing climate-related disturbances. Nutrients from seabirds nesting on oceanic islands enhance the productivity and functioning of adjacent coral reefs, but it is unknown whether these subsidies affect the response of coral reefs to mass bleaching events or whether the benefits of these nutrients persist following bleaching. To answer these questions, we surveyed benthic organisms and fishes around islands with seabirds and nearby islands without seabirds due to the presence of invasive rats. Surveys were conducted in the Chagos Archipelago, Indian Ocean, immediately before the 2015–2016 mass bleaching event and, in 2018, two years following the bleaching event. Regardless of the presence of seabirds, relative coral cover declined by 32%. However, there was a post-bleaching shift in benthic community structure around islands with seabirds, which did not occur around islands with invasive rats, characterized by increases in two types of calcareous algae (crustose coralline algae [CCA] and Halimeda spp.). All feeding groups of fishes were positively affected by seabirds, but only herbivores and piscivores were unaffected by the bleaching event and sustained the greatest difference in biomass between islands with seabirds versus those with invasive rats. By contrast, corallivores and planktivores, both of which are coral-dependent, experienced the greatest losses following bleaching. Even though seabird nutrients did not enhance community-wide resistance to bleaching, they may still promote recovery of these reefs through their positive influence on CCA and herbivorous fishes. More broadly, the maintenance of nutrient subsidies, via strategies including eradication of invasive predators, may be important in shaping the response of ecological communities to global climate change.