The dataset contains records of bats (Chiroptera) collected in the lower valley of River Sabor, in the scope of the long-term Ecological Monitoring Program (PME) of the Baixo Sabor Hydroelectric Dams, promoted by EDP – Energias de Portugal, S.A. Data were collected between July 2012 and August 2014, during field visits to 12 known bat hibernation, reproduction and pre-dispersion (post-reproduction) roosts with restricted access (caves and mine entrances). These roosts were located within a 5-km radius buffer around the lower valley of River Sabor. The presence and identity of the bat species were assessed by acoustic sampling of the echo-location calls emitted in flight. The records include taxa identified at the species, genus, family or order level, as well as several potential species present in 2 acoustic “species complexes”. 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 (undergraded) coordinates may be provided upon request by the resource contact from EDP, who will define the terms and conditions for its use.