Bats are considered important bioindicators and deliver key ecosystem services to humans. However, it is not clear how the individual and combined effects of climate change and land-use change will affect their conservation in the future. We used a spatial conservation prioritization framework to determine future shifts in the priority areas for the conservation of 169 bat species under projected climate and land-use change scenarios across Africa. Specifically, we modelled species distribution models under four different climate change scenarios at the 2050 horizon. We used land-use change scenarios within the spatial conservation prioritization framework to assess habitat quality in areas where bats may shift their distributions. Overall, bats’ representation within already existing protected areas in Africa was low (∼5% of their suitable habitat in protected areas which cover ∼7% of Africa). Accounting for future land-use change resulted in the largest shift in spatial priority areas for conservation actions, and species representation within priority areas for conservation actions decreased by ∼9%. A large proportion of spatial conservation priorities will shift from forested areas with little disturbance under present conditions to agricultural areas in the future. Planning land use to reduce impacts on bats in priority areas outside protected areas where bats will be shifting their ranges in the future is crucial to enhance their conservation and maintain the important ecosystem services they provide to humans.