Passive forest restoration can buffer the effects of habitat loss on biodiversity. We acoustically surveyed aerial insectivorous bats in a whole‐ecosystem fragmentation experiment in the Brazilian Amazon over a 2‐year period, across 33 sites, comprising continuous old‐growth forest, remnant fragments, and regenerating secondary forest matrix. We analyzed the activity of 10 species/sonotypes to investigate occupancy across habitat types and responses to fragment size and interior‐edge‐matrix (IEM) disturbance gradients. Employing a multiscale approach, we investigated guild (edge foragers, forest specialists, flexible forest foragers, and open space specialists) and species‐level responses to vegetation structure and forest cover, edge, and patch density across six spatial scales (0.5–3 km). We found species‐specific habitat occupancy patterns and nuanced responses to fragment size and the IEM disturbance gradient. For example, Furipterus horrens had lower activity in secondary forest sites and the interior and edge of the smallest fragments (1 and 10 ha) compared to continuous forest, and only two species (Pteronotus spp.) showed no habitat preference and no significant responses across the IEM and fragment size gradients. Only the Molossus sonotype responded negatively to vegetation structure. We uncovered no negative influence of forest cover or edge density at guild or species‐level. Our results indicate that reforestation can buffer the negative effects of fragmentation and although these effects can still be detected in some species, generally aerial insectivorous bats appear to be in recovery after 30 years of passive forest restoration. Our findings reinforce the need to protect regenerating forests while conserving vast expanses of old‐growth forest.