The seasonal use of caves by bats can be attributed to physiologically demanding activities like mating and reproduction in spring and torpor in winter. Cave use, however, varies within and across species and can depend on the physical and microclimatic conditions of the caves. Understanding the current patterns and predictors of cave use is therefore crucial to develop a reference for assessing the response of bats to future changes in climatic conditions. We quantified the diversity and abundance of bats in 41 caves that varied in structure and temperature across a seasonal (mid-winter, late-winter and early-spring) and an elevational (400–2700 m above sea level) gradient in the central Himalayas. Richness and abundance of bat species exhibited seasonal variation, with more species and individuals present in caves during early-spring (n = 15) compared to mid-winter (n = 9). Species richness declined linearly with elevation in mid-winter but remained relatively similar until 900 msl and then declined in late-winter and early-spring. 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 within caves during early-spring compared to mid-winter. The season- and species-specific cave use that we report here suggests that even minor fluctuations in cave temperatures could potentially alter the composition of bat communities inside caves. Prioritization assessment based on a bat cave vulnerability index indicates that different caves must be protected based on their specific usage patterns and the abundance of species they support at various times. Overall, we highlight the importance of studying cave-dwelling bats in climate-vulnerable areas such as the Himalayas where species richness is high to help understand and predict the responses of animals to climate change.