The goals of the present study were to determine (1) how low-intensity selective logging in the southeastern Amazon alters several habitat features proposed to be important to bats, and (2) whether changes to habitat variables were correlated to changes in bat species composition, bat abundances, and trophic structure. Bats were captured using a standardized number of mistnets set in the understory and the canopy in 1-ha study grids located in logged (n = 5) and unlogged (n = 5) forest. A total of 1,235 individuals were captured, representing six families, 35 genera, and 58 species. Abundances of nectarivorous and frugivorous taxa within the Glossophaginae, Lonchophyllinae, Stenodermatinae, and Carolliinae were higher in logged sites where canopy openness and understory foliage density were greatest. In contrast, insectivorous and omnivorous species within the Emballonuridae, Mormoopidae, Phyllostominae, and Vespertilionidae were more abundant in unlogged sites where canopy foliage density and variability in the understory stratum were greatest. The results suggest that low-intensity logging modifies a number of habitat features that appear to be important to some taxa, leading to changes in bat community and trophic structure.