Biological invasions pose a threat to nearly every ecosystem worldwide.1,2 Although eradication programs can successfully eliminate invasive species and enhance native biodiversity, especially on islands,3 the effects of eradication on cross-ecosystem processes are unknown. On islands where rats were never introduced, seabirds transfer nutrients from pelagic to terrestrial and nearshore marine habitats, which in turn enhance the productivity, biomass, and functioning of recipient ecosystems.4–6 Here, we test whether rat eradication restores seabird populations, their nutrient subsidies, and some of their associated benefits for ecosystem function to tropical islands and adjacent coral reefs. By comparing islands with different rat invasion histories, we found a clear hierarchy whereby seabird biomass, seabird-driven nitrogen inputs, and the incorporation of seabird-derived nutrients into terrestrial and marine food chains were highest on islands where rats were never introduced, intermediate on islands where rats were eradicated 4–16 years earlier, and lowest on islands with invasive rats still present. Seabird-derived nutrients diminished from land to sea and with increasing distance to rat-eradicated islands, but extended at least 300 m from shore. Although rat eradication enhanced seabird-derived nutrients in soil, leaves, marine algae, and herbivorous reef fish, reef fish growth was similar around rat-eradicated and rat-infested islands. Given that the loss of nutrient subsidies is of global concern,7 that removal of invasive species restores previously lost nutrient pathways over relatively short timescales is promising. However, the full return of cross-ecosystem nutrient subsidies and all of their associated demographic benefits may take multiple decades.