The Brazilian Cerrado is a Neotropical savanna extremely threatened by human-driven habitat changes while simultaneously one of the formations with the highest degree of floristic endemism in the world. In the last decades, more than half of the Cerrado area has been converted by agriculture and livestock production, leading to a significant loss of its natural vegetation. Here we evaluated changes in bat diversity between varying agricultural land use intensity levels and phytophysiognomies of the Cerrado. Because processes behind the patterns of community assembly act on ecological redundancies and complementarities of organisms and not only, or necessarily, on the number of species present in a certain region, we focused on taxonomic, functional and phylogenetic diversity of bats. We predicted that all three dimensions of bat diversity were negatively correlated with increasing levels of land-use intensity in the Cerrado, and that this pattern was mirrored in distinct phytophysiognomies of the domain. We sampled bats in the central Brazilian Cerrado using a comprehensive sampling scheme of mist-nets and automated real-time ultrasound-recording units in 27 sampling points covering different physiognomies and levels of land-use modification for two consecutive years. To our knowledge our sampling was unique in combining these two techniques, returning information on close-, edge- and open-space foraging guilds, rarely all sampled in Neotropical bat studies. A remarkable total of 64 species of six families were registered in the study area. In general no statistical differences were found in any of the diversity metrics between the sampled physiognomies, but a decrease in taxonomic, functional and phylogenetic diversity was observed in all physiognomies associated with land use intensification and this was consistent across guilds. This demonstrates the potential negative impact of land use intensification in ecosystem services provided by bats, including pollination, seed dispersal and insect control