Across the globe, millions of hectares of native vegetation have been replaced by commercial plantations, with negative consequences for biodiversity. The effects of the replacement of native vegetation with commercial plantations on the functional and phylogenetic diversity of bat assemblages remain understudied, and most studies have focused exclusively on the taxonomic component of diversity. Here, we investigate how the replacement of natural savannahs by acacia plantations affects the α- and β-diversity of bat assemblages. We sampled bats, using mist-nets at ground level, in natural forest, savannah areas and acacia plantations, in the Lavrados de Roraima in the northern Brazilian Amazon. Our results show that, in general, acacia is less diverse than native forests in terms of taxonomic and functional diversity, and is also less taxonomically diverse than the savannah matrix which it substitutes. The observed patterns of α- and β-diversity found in the present study are in large part driven by the superabundance of one generalist and opportunistic species,Carollia perspicillata, in the acacia plantations. Taken together, our results show that the replacement of areas of natural savannah by acacia plantations causes a regional loss in diversity across all diversity dimensions: taxonomic, functional and phylogenetic. However, further studies are required to fully understand the ecological and conservation implications of this landscape change.