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Islands exhibit disproportionally high biodiversity, however high levels of endemism and simplified food webs make their communities susceptible to invasive species. Introduced goats (Capra hircus), a generalist herbivore, are among the most harmful invasive species on islands. Concern about goat impacts on island communities have resulted in eradication programs, which have been generally implemented without comprehensive evaluation and monitoring. Unintended consequences may follow eradication, as grazing can have complex effects on island food webs. Using whole island manipulations, we evaluate the long-term, community-wide effects of goat herbivory, as well as their subsequent removal, in a system of 16 islands in the Aegean Sea (Greece) located within the Mediterranean biodiversity hotspot. Goat grazing on these islands is a major conservation concern, as these support endemic plant communities that have evolved in low herbivory conditions and lack appropriate defenses. We show that goat introductions lead to significant decreases in vegetation height, percent cover, and biomass but not to immediate plant species loss, as native island endemics are replaced with widespread generalist taxa carried in by the livestock. Additionally, goats contribute to the desertification of islands by initiating a long-term soil loss cycle that continues even after goats are removed; however, remaining soil structure and chemistry are not affected. Island arthropod populations do not appear to be significantly impacted by goat introduction or removal, except for a distinct increase in the order Diptera with goat presence. This study also reaffirms the role of seabirds in providing important marine subsidies, rich in nitrogen and phosphorus, to island food webs. Plant species diversity declines following goat removal, and vegetation cover returns only partially, as further recovery is being prevented by the long-term loss of soil. This suggests that following goat removal, island communities may require additional restoration efforts, including seabird reestablishment and reintroduction of extirpated plant populations, to promote island recovery.