The seasonal use of caves by bats can be attributed to physiologically demanding activities like mating and reproductions or torpor. Although cave use varies intra- and inter-specifically in bats, the microclimatic characteristics of roost sites have significant implications for the fitness of bat populations. As these microclimates are increasingly influenced by surface level climatic changes, understanding the current patterns of cave utilization is crucial to assess the impact of climate change on bats. Therefore, we monitored cave temperatures and studied the diversity and abundance of bats in 41 caves across a seasonal (mid-winter, late-winter and early-spring) and an elevational (400 to 2700 meters above sea level) gradient in the Central Himalayas. The richness and abundance of bat species exhibited seasonal variations, with more species and individuals present during early spring (n = 15) compared to mid-winter (n = 9). Species richness exhibited a linear decline with elevation in mid-winter, but remained relatively stable until 900 msl and then declined in late-winter and early-spring. Furthermore, species such as Hipposideros armiger (20.14 ± 1.60°C in spring and 17.97 ± 0.88°C in mid-winter), Rhinolophus affinis (19.98 ± 1.76°C in spring and 16.18 ± 3.09°C in mid-winter) and Rhinolophus cf. pusillus (19.55 ± 1.64°C in spring and 15.43 ± 2.87°C in mid-winter) preferred warmer microclimates during early-spring compared to mid-winter. This season- and species- specific cave use suggests that even minor fluctuations in cave temperatures could potentially alter the composition of bat communities inside caves. We recommend that long-term studies in such highly diverse climate vulnerable areas would help understand and predict the responses of cave-dwelling bats to climate change.