Habitat fragmentation is considered as major threat to biodiversity worldwide. Biodiversity can be described as taxonomic, functional and phylogenetic diversity. However, the effect of forest fragmentation on taxonomic, phylogenetic and functional diversity is barely understood. We compare the response of taxonomic (species richness), phylogenetic and functional diversity of birds to forest fragmentation. We hypothesised that with increasing forest patch isolation and/or decreasing patch size the diversity of birds decreases but only if certain thresholds of fragmentation metrics are reached. Specifically, we hypothesized that out of the three diversity components the taxonomic diversity is the most sensitive to forest fragmentation, which means that it starts declining at larger patch size and higher connectivity values than phylogenetic and functional diversity do. We compared the three biodiversity metrics of central European bird species in a large set of forest patches located in an agricultural landscape. General additive modeling and segmented regression were used in analyses. Habitat fragmentation differentially affected studied biodiversity metrics. Bird taxonomic diversity was the most responsive towards changes in fragmentation. We observed an increase in taxonomic diversity with increasing patch area, which then stabilized after reaching certain patch size. Functional diversity turned out to be the least responsive to the fragmentation metrics and forest stand characteristics. It decreased linearly with the decreasing isolation of forest patches. Apart from the habitat fragmentation, bird taxonomic diversity but not phylogenetic diversity was positively associated with forest stand age. The lower share of dominant tree species, the highest taxonomic diversity was. While preserving a whole spectrum of forests (in terms of age, fragmentation and size) is important from the biodiversity perspective, forest bird species might need large, intact, old-growth forests. Since the large and intact forest becomes scarcer, our study underscore their importance for the preservation of forest specialist species.