Despite recent interest in understanding the effects of human-induced global change on carbon (C) storage in terrestrial ecosystems, most studies have overlooked the influence of a major element of global change, namely biological invasions. We quantified ecosystem C storage, both above- and below-ground, on each of 18 islands off the coast of New Zealand. Some islands support high densities of nesting seabirds, while others have been invaded by predatory rats and host few seabirds. Our results show that, by preying upon seabirds, rats have indirectly enhanced C sequestration in live plant biomass by 104%, reduced C sequestration in non-living pools by 26% and increased total ecosystem C storage by 37%. Given the current worldwide distribution of rats and other invasive predatory mammals, and the consequent disappearance of seabird colonies, these predators may be important determinants of ecosystem C sequestration.