Boreal caribou require large areas of undisturbed habitat for persistence. They are listed as threatened with the risk of extinction in Canada because of landscape changes induced by human activities and resource extraction. Here we ask: Can the protection of habitat for boreal caribou help Canada meet its commitments under the United Nations Convention on Biological Diversity and United Nations Framework Convention on Climate Change? We identified hotspots of high conservation value within the distribution of boreal caribou based on: (1) three measures of biodiversity for at risk species (species richness, unique species and taxonomic diversity); (2) climate refugia or areas forecasted to remain unchanged under climate change; and, (3) areas of high soil carbon that could add to Canada’s greenhouse gas emissions if released into the atmosphere. We evaluated the overlap among hotspot types and how well hotspots were represented in Canada’s protected and conserved areas network. While hotspots are widely distributed across the boreal caribou distribution, with nearly 80% of the area falling within at least one hotspot type, only 3% of the distribution overlaps three or more hotspots. Moreover, the protected and conserved areas network only captures about 10% of all hotspots within the boreal caribou distribution. While the protected and conserved areas network adequately represents hotspots with high numbers of at risk species, areas occupied by unique species, as well as the full spectrum of areas occupied by different taxa, are underrepresented. Climate refugia and soil carbon hotspots also occur at lower percentages than expected. These findings illustrate the potential co-benefits of habitat protection for caribou to biodiversity and ecosystem services and suggest caribou may be a good proxy for future protected areas planning and for developing effective conservation strategies in regional assessments.