Individual movements of bats result from a compromise between their recognition of the environment and their potential to fulfill bats’ life requirements, and to the potential threats associated with moving, all of this is mediated by habitat selection. Mining activities produce modifications to the environments that add heterogeneity and fragmentation to the landscapes used by bats, with overall poorly understood consequences to their movements and to the underground-related biodiversity. Cave dwelling bats spend a large part of their life cycle within their roosts, and they are of paramount importance to the subterranean biodiversity because of their constant movements between the external landscapes, which they selectively use, and the underground ecosystems, where they usually apport energy in form of organic matter. We investigated the variation of patterns of habitat use and selection by cave-dwelling bats in a mosaic of disturbed and conserved Eastern Amazonian forests and rupestrian iron-rich savannas (cangas) interspersed in an extensive iron-caves system. We studied the movements of two phylogenetically distant related insectivores, the aerial insect-catcherFuripterus horrens(Furipteridae) and the foliage gleaning batLonchorhina aurita(Phyllostomidae), both cave-dependent in the study area, one of them categorized as threatened to extinction in Brazil, and virtually unknown in terms of their movement behavior, and habitat use. We used radio telemetry to assess habitat use, under the prediction that these species prefer natural and conserved habitats for their foraging bouts, avoiding human-modified habitats. We also anticipated larger range-areas and commuting distances for both species when foraging in disturbed landscapes. Thirty-one bats were monitored in different landscapes (conserved Amazonian ombrophilous forests and cangas, mining sites and pasture) resulting in an average range of 346.9 ± 762.5 ha and an average commuting distance of 1921.5 ± 2269.7 m forF. horrensand of 716.8 ± 1000.6 ha and 2582.2 ± 1966.0 m forL. aurita. Our habitat selection analyses suggest thatFuripterus horrensis an open space forager, with individuals frequently recorded foraging in cangas, andL. auritais a forest forager, although using all habitats proportionally to their availability in the landscape. We did not detect landscape-related effects to the use of space by both species, whereas seasonal variation emerged as a relevant effect. This is the first time that movement data forF. horrensandL. auritais presented. Our study delivers original baseline data on movement behavior and conservation of these threatened cave-dwelling bat species with virtually unknown biology and shed light into constraints related to the optimal and adjusted biological cycles of the bats and their range areas under scenarios of disturbance.