Human landscape alterations and invasions by non-native species are one of the main causes of biodiversity loss. The predicted effect of indigenous species extinctions and exotic species colonisation is the increase of biotic homogenisation in human-altered landscapes. This process is accentuated on isolated oceanic islands where numerous empty niche opportunities are offered. To assess the role of exotic species in biotic homogenisation, we sampled epigean and canopy arthropod assemblages in four islands of the Azores archipelago. Habitats were selected across a disturbance gradient from native forests to most disturbed agricultural areas. We detected that exotic species promote assemblage homogenisation. Interestingly, such process was contingent on each island and habitat. We also analysed the degree of nestedness, which represents the extent of ordered loss/gain of species across environmental or ecological gradients. On the contrary, species can show segregation characterising their species replacement across such gradients. We detected that both exotic and indigenous species may show segregated patterns, indicating distinct local assemblages. Thus, exotic species also show habitat specialisation, not necessarily contributing to the homogenisation of regional fauna. We also detected that in most disturbed agricultural habitats, the species richness of both indigenous and exotic species was drastically reduced. However, only exotics showed low species richness in native forests, suggesting that native assemblages may have a degree of resistance to invasions in undisturbed habitats. Concluding, habitat disturbance seems to be a key factor structuring both epigean and canopy assemblages in the Azores archipelago.