The Albertine Rift is one of Africa’s most biodiverse regions but is threatened by habitat loss as a result of agricultural expansion and human development. Previous studies estimated that 30% of the region has been lost to agricultural conversion and we estimate here that 33% is allocated for mining concessions. For conservation planning, we used niche models for species endemic to the Albertine Rift and those that are globally threatened. We assessed where to conserve these species using three scenarios: (1) a baseline assuming equal conservation costs across all grid cells in the study area, (2) a scenario locking in existing protected areas (i.e. always selecting them by default) and assessing which unprotected areas require conservation, and (3) a scenario considering mining planned across the region. Marxan analyses produced similar results for the three scenarios, highlighting the importance of existing protected areas and the value of several community-managed or provincial protected areas in the eastern Democratic Republic of the Congo. The current protected area network covers 134,246 km2 and an additional 64,586 km2 would be required to ensure the conservation of all threatened and endemic species outside the parks and wildlife reserves. However, if trying to avoid mining concessions this increases to 145,704 km2, an area larger than the existing protected areas. Some mining concessions harbor species with a restricted range and would thus need to be protected to ensure the persistence of threatened and endemic fauna and flora. These mining concessions should be challenged by the conservation community.