Fruit bats serve as crucial bioindicators, seed dispersers, pollinators, and contributors to food security within ecosystems. However, their population and distribution were threatened by climate change and anthropogenic pressures. Understanding the impacts of these pressures through mapping distribution and habitat suitability is crucial for identifying high‐priority areas and implementing effective conservation and management plans. We predicted the distribution and extent of habitat suitability for Rousettus aegyptiacus and Epomophorus labiatus under climate change scenarios using average predictions from four different algorithms to produce an ensemble model. Seasonal precipitation, population index, land‐use land cover, vegetation, and the mean temperature of the driest quarter majorly contributed to the predicted habitat suitability for both species. The current predicted sizes of suitable habitats for R. aegyptiacus and E. labiatus were varied, on average 60,271.4 and 85,176.1 km2, respectively. The change in species range size for R. aegyptiacus showed gains in suitable areas of 24.4% and 22.8% in 2050 and 2070, respectively. However, for E. labiatus, suitable areas decreased by 0.95% and 2% in 2050 and 2070, respectively. The range size change of suitable areas between 2050 and 2070 for R. aegyptiacus and E. labiatus shows losses of 1.5% and 1.2%, respectively. The predicted maps indicate that the midlands and highlands of southern and eastern Ethiopia harbor highly suitable areas for both species. In contrast, the areas in the northern and central highlands are fragmented. The current model findings show that climate change and anthropogenic pressures have notable impacts on the geographic ranges of two species. Moreover, the predicted suitable habitats for both species are found both within and outside of their historical ranges, which has important implications for conservation efforts. Our ensemble predictions are vital for identifying high‐priority areas for fruit bat species conservation efforts and management to mitigate climate change and anthropogenic pressures.