Assessing where wildlife populations are at risk from future habitat loss is particularly important for land-use planning and avoiding biodiversity declines. Combining projections of future deforestation with species density information provides an improved way to anticipate such declines. Using the critically endangered Bornean orangutan (Pongo pygmaeus) as a case study we applied a spatio-temporally explicit deforestation model to forest loss data from 2001 to 2017 and projected future impacts on orangutans to the 2030s. Our projections point to continued deforestation across the island, amounting to a potential loss of forest habitat for 26,200 orangutans. Populations currently persisting in forests gazetted for industrial timber and oil palm concessions, or unprotected forests outside of concessions, were projected to experience the worst losses within the next 15 years, amounting to 15,400 individuals. Our analysis indicates the importance of protecting orangutan habitat in plantation landscapes, maintaining protected areas and efforts to prevent the conversion of logged forests for the survival of highly vulnerable wildlife. The modeling framework could be expanded to other species with available density or occurrence data. Our findings highlight that species conservation should not only act on the current information, but also anticipate future changes to be effective.