We studied the distribution of an endangered species of bat strongly associated with woods in NW Italy. A species distribution model (SDM) was built on data collected in 2015–2016 using a presence-only technique (maximum entropy) incorporating environmental variables (19 habitat categories, and 4 topography variables). Barbastelle bat presence (132 sites) was associated with woods (beechwoods, oak-hornbeam woods, and wood arboriculture), while there was a negative selection of built or cultivated areas and open space categories. The model was highly successful when predicting the presence/absence of the species in 43 new sites sampled in 2017–2018. SDM was utilized to calculate resistance surfaces and to assess potential suitable connections among the currently utilized areas. The currently protected areas of NW Italy showed a moderate overlap both with high environmental value areas (23.5%) or high connection areas (11.3%). This study highlights a moderate effectiveness of the protected areas network for conservation of barbastelle bat, and suggests preventing land-use change in current woodland areas and increasing connections in the lowland areas of the region. Our results from predicted species occurrence obtained through SDM can be utilized for targeting survey efforts to identify new barbastelle bat sites.