Human-induced environmental changes, such as the introduction of invasive species, are driving declines in the movement of nutrients across ecosystems with negative consequences for ecosystem function. Declines in nutrient inputs could thus have knock-on effects at higher trophic levels and broader ecological scales, yet these interconnections remain relatively unknown. Here we show that a terrestrial invasive species (black rats, Rattus rattus) disrupts a nutrient pathway provided by seabirds, ultimately altering the territorial behaviour of coral reef fish. In a replicated ecosystem-scale natural experiment, we found that reef fish territories were larger and the time invested in aggression lower on reefs adjacent to rat-infested islands compared with rat-free islands. This response reflected changes in the economic defendability of lower-quality resources, with reef fish obtaining less nutritional gain per unit foraging effort adjacent to rat-infested islands with low seabird populations. These results provide a novel insight into how the disruption of nutrient flows by invasive species can affect variation in territorial behaviour. Rat eradication as a conservation strategy therefore has the potential to restore species interactions via territoriality, which can scale up to influence populations and communities at higher ecological levels.