We identified several ecological parameters that may promote the foraging habitat differentiation by sympatric bat species. The exploitation of discrete habitats was shown to facilitate the coexistence of morphologically similar species. Bats represent a model species group, where many morphologically similar species exploit similar resources, e.g. insects as prey organisms. We studied three closely related species of bats in a Central European region of sympatric occurrence — the common pipistrelle (Pipistrellus pipistrellus), Nathusius’ pipistrelle (P. nathusii), and the soprano pipistrelle (P. pygmaeus). We employed point locality data and niche-based species distribution modelling (maximum entropy modelling, ‘MaxEnt’) to model the habitat use by these species. A restricted distribution of P. pygmaeus and P. nathusii compared to P. pipistrellus was observed that may indicate a stronger habitat specialization of these two species compared to P. pipistrellus. Land cover, as well as several climatic variables influenced the habitat use of all three species (e.g., the precipitation in spring, and the temperature minimum in late summer). Despite an overlap in foraging habitat parameters, differences among species concerning their preferred habitat were noted. Responses to isothermality, mean diurnal range of temperature, temperature seasonality, and land cover differed among species. The data identify microclimatic factors, besides vegetation and other land cover types, as important effectors for habitat partitioning in these three Pipistrellus species.