AimTo investigate the influence of ecological factors, geologic and climatic history on current diversity patterns of bat communities. We predicted that (i) our three different biodiversity dimensions (species richness, functional and phylogenetic diversity) will have a positive relationship with habitat heterogeneity; (ii) variation in phylogenetic diversity will be positively influenced by elevation; (iii) biodiversity dimensions will be influenced by climatic stability, with less diversity in regions with higher climatic instability.LocationNeotropical Savannah (Cerrado).MethodsWe calculated nine metrics: species richness, functional diversity, phylogenetic diversity, mean paired functional distance (MFD) and phylogenetic distances (MPD), richness‐corrected functional diversity (SES‐FD), richness‐corrected phylogenetic diversity (SES‐PD) and richness‐corrected mean functional and phylogenetic distances (SES.MFD and SES.MPD) using distribution records for 111 bat species. Habitat heterogeneity, climatic variables, elevation, floristic and climatic stability were used as independent variables. We used hierarchical Bayesian models to spatialise biodiversity dimensions based on the best predictors.ResultsCerrado habitat heterogeneity is important for phylogenetic diversity and mean functional and paired phylogenetic distances. Precipitation, temperature, elevation, habitat heterogeneity, and climatic stability were the most important predictors of Cerrado bat biodiversity. Species richness is inversely related to climatic instability, which is the best predictor of this metric. There is a decline in species richness in regions where the floristic composition has been more altered during the last 30,000 years, mainly in southern Cerrado.Main ConclusionsPresent‐day and historical factors simultaneously explain the biodiversity dimensions of bat communities in the Cerrado. Habitat heterogeneity is a major driver of phylogenetic diversity of Cerrado bats, and species of closely related lineages share habitats with homogeneous vegetation. Cerrado climatic changes and geologic history influenced the observed diversity metrics (PD and FD) and the ones corrected for species richness (SES‐PD and SES‐FD) in opposite ways. Species richness corrected metrics (SES‐PD and SES‐FD) indicate that species filtered by adaptive traits mainly occupied regions of climatic instability.