With approximately 1,400 known species, 184 of which are found in Brazil, the order Chiroptera is the second most diverse among mammals, and this taxon is relevant in terms of the ecosystem services it provides to humans. However, disturbances caused by anthropogenic factors amplify processes of extinction, changes in geographic distributions, and phenological alterations in species, despite efforts to protect biodiversity and its resources through the creation and establishment of Conservation Units, in addition to Indigenous Lands. Nevertheless, taxonomic knowledge gaps or geographical distribution challenges pose obstacles to the effective implementation of conservation strategies in areas designated for biodiversity protection. Therefore, this study evaluates the contribution of Brazilian Conservation Units (Full Protection Units and Sustainable Use Units) and Indigenous Lands to the protection of bat species and ecosystem services in Brazil. It also presents maps of richness by trophic guilds and threat classification according to IUCN, including species classified as Data Deficient. The results indicated low percentages of areas within Conservation Units and Indigenous Lands with the potential distribution of bats, especially for insectivorous, nectarivorous, and frugivorous guilds in the Cerrado, classified as Near Threatened. Additionally, higher bat richness was observed in the Amazon and Atlantic Forest.