The IUCN has listed the long-whiskered owlet (Xenoglaux loweryi) as vulnerable due to the presence of few geographic records, its restricted range, and anthropogenic threats. Its natural history and ecology are largely unknown, and its distribution is widely debated; therefore, there is an urgent need for the real-time conservation of X. loweryi. In this study, 66 geo-referenced records of X. loweryi, 18 environmental variables, and the maximum entropy model (MaxEnt) have been used to predict the current and future (2050 and 2070) potential distribution of X. loweryi in the Amazonas and San Martin regions of northwestern Peru. In fact, under current conditions, areas of “high”, “moderate”, and “low” potential habitat suitability cover 0.16% (140.85 km2), 0.46% (416.88 km2), and 1.16% (1048.79 km2) of the study area, respectively. Moreover, under future conditions, the “high”, “moderate”, and “low” probability areas present profits and losses in terms of habitat suitability. Based on the environmental variables, this species mostly inhabits areas with a forest fraction with presence of trees with an emergent tree canopy of ~10–30 metres and depends on Yunga montane forest habitats with high humidity but it is not dependent on bare cover area, crops, or grasslands. Nevertheless, most of the current and future distribution areas are not part of the protected natural areas of Amazonas and San Martin. Additionally, the combination of climate change and anthropogenic activities contribute to further losses of this species habitat. Therefore, from the management point of view, corrective and preventive actions will help to preserve this species over time.