The Amazon region is made up of a mosaic of important habitats scattered throughout the rainforests, which differ in vegetation structure, basal area, primary productivity, biomass and production of flowers and fruits. Consequently, species richness and abundance also vary between these habitat types, in part explaining the high levels of richness found in the Amazon region. Here, we sampled bats using mist nets in three Amazonian habitats to explore variation in richness, abundance and community composition between habitats and seasons, and test for variation in the number and composition of bats captured in different mist net shelves. Overall abundance was highest in Amazonian savannahs, which is probably due to these habitats being more complex at the landscape scale — being composed of areas of savannah interspersed with forest fragments, gallery forests and palm stands. Abundance was also higher in the rainy season in savannahs and terra firme forest, and in the dry season in campinarana. In all habitats, bats were most frequently captured between 0.7 and 2.4 m from the ground. These results have important implications for our understanding of the ecology of, and habitat use by bats in the Amazon, particularly in the less well-studied habitat types of Amazonian savannah and campinarana. In addition, knowledge of the distribution of bat captures between mist net shelves serves to highlight that nets need not be set so close to the ground to maintain sampling efficiency, which is important as it may help to reduce opportunistic predation events of individuals caught in the lowest mist net shelf.