Seabirds can strongly affect several major factors correlated with species diversity by concentrating marine nutrients on their nesting islands and by physically disturbing island vegetation. In this study, we investigated the effects of nesting cormorants on the abundance, species richness, and composition of plants and arthropods (Coleoptera, Heteroptera, Araneae, and Chironomidae) on islands in Stockholm archipelago, Sweden. Nesting cormorants negatively affected plant species richness and vegetation cover and that changed plant species composition. The effect of nesting cormorants on island arthropods varied between feeding groups and sampling methods. Most orders did not change in abundance or species richness but some, such as coleopterans and spiders changed in species composition. Herbivorous coleopterans were generally negatively affected by cormorants whereas fungivorous species and scavengers were generally positively affected. In structural equation modeling we found that the effect of cormorants was sometimes direct, such as on scavengers, but many effects on island consumers were mediated by changes in vegetation caused by cormorant presence. Overall, arthropod communities were highly dissimilar between cormorant and reference islands, and we therefore conclude that nesting cormorants not only affect the diversity of their nesting islands but also of the archipelago as a whole. The total diversity in the archipelago may increase through regional increased habitat heterogeneity and by adding species which are favored by seabirds (e.g. scavenging and fungivorous coleopterans).