Hydroelectric dams have proliferated across the tropics, leading to extensive landscape changes driven by habitat loss and fragmentation of lowland forests. Assessing their effects on biodiversity and designing effective conservation strategies require a comprehensive understanding of both the local habitat context and landscape-scale perspective. We investigated the influence of local, patch and landscape-scale variables on the taxonomic, functional, and phylogenetic diversity of aerial insectivorous bats in a 30-year-old archipelagic forest landscape in Brazilian Amazonia. Bats were surveyed using passive recorders across 28 forest islands and six adjacent continuous forest sites. Taxonomic, functional, and phylogenetic diversity facets were calculated within a Hill numbers approach that considers the importance of rare, common, and dominant species. We analyzed the response of bat diversity to both local and landscape changes, using vegetation structure, patch, and landscape variables as predictors. Taxonomic, functional, and phylogenetic diversities were reduced on forest islands. All facets of diversity for species richness (q = 0) and common species (q = 1) were positively influenced by local and patch-scale characteristics, including tree species diversity and forest cover, but negatively affected by edge area around the islands. Taxonomic diversity was found to be a good indicator of phylogenetic diversity. Undisturbed continuous forests and islands that support species-rich tree floras and lower edge habitat density, harboured greater numbers of aerial insectivorous bats, as well as phylogenetically diverse assemblages exhibiting broader ecological functions. Bat diversity was most influenced by habitat quality, highlighting the need to establish protected forest areas that include large islands (>100 ha) around land bridge island systems.