The dataset contains records of bats (Chiroptera) collected in roosts along the lower valley of River Sabor, in the scope of the Ecological Monitoring (PME) and Mitigation/Compensation Measures (PMC) Programs of the Baixo Sabor Hydroelectric Dams, promoted by EDP – Energias de Portugal, S.A. Data were collected between February 2015 and February 2020, during field visits to 266 known bat roosts, both natural (caves, mines, tunnels, bridges, buildings, etc.) and newly-built/recovered, within the scope of PMC (an underground roost built near the dam, adapted pigeon lofts and mines, sealed mines, and shelter boxes) for hibernation and reproduction, within a 5-km radius around the lower valley of River Sabor. The presence of individuals was recorded by direct observation. The records include taxa identified at the species or genus level. In one occasion it was not possible to discriminate the species, so they were grouped in a “species complex” of two species of the same genus. More than 55,000 individuals of 20 taxa (17 species and 3 genus/”species complexes”) were recorded in 2,080 observation events. Due to the vulnerability of the roost locations, the precision of the geographic coordinates was degraded to 0.01, according to the recommendations of Chapman & Grafton (2008). The dataset with the original (undegraded) coordinates may be provided upon request by the resource contact from EDP, who will define the terms and conditions for its use.