Habitat fragmentation and conversion are among the human activities that pose the greatest threat to species persistence and conservation of biodiversity. This is particularly true in the Neotropics, where bats represent important components of biodiversity from taxonomic and functional perspectives, and provide critical ecosystem services (e.g., seed dispersal and pollination). We assessed the degree to which conversion of lowland Amazonian rain forest to agriculture, and its subsequent abandonment and secondary succession, affect the abundances of populations of phyllostomid bats in the vicinity of Iquitos, Perú. During 90,720 net-m-h of sampling, we captured 3789 bats of five families; of these 3764 were phyllostomids representing 44 species, 23 genera, and three feeding guilds. We focus on the 24 most abundant species of phyllostomids. In terms of abundance, frugivores dominated assemblages in all habitat types and seasons. Eight species consistently responded to habitat conversion, two species consistently responded to season, two species responded consistently to both habitat and season, and five species responded to habitat conversion in a season-specific manner. Frugivores and nectarivores were abundant in areas that had been converted to agriculture, which suggests that these bats are resilient to extant levels of disturbance and may be important in promoting secondary succession. However, this result may be scale- or context-dependent. If habitat conversion continues and dramatically reduces the areal extent and increases fragmentation of mature forest, then a complex metacommunity dynamic may characterize the region and source populations of bats may become threatened or extirpated locally.