The persistence of threatened wildlife species depends on successful conservation and restoration of habitats, but climate change and other stressors make these tasks increasingly challenging. Applying climate change vulnerability analyses to contemporary wildlife management can be difficult because most analyses predict direct effects of future climate on wildlife species at broad geographic scales, rather than assessing their habitats at local scales (<1 km) that correspond to site-specific habitat management actions. We present a framework that synthesizes vegetation-focused vulnerability assessments to assess multiple effects on wildlife species' diverse habitat needs, providing a scenario-driven climate vulnerability assessment that maps differences in vulnerability of populations within a species' range. Our flexible habitat-centered synthesis approach leverages available spatial datasets describing projected exposure to vegetation changes due to climate change and other potentially synergistic stressors, reclassifies and weights them based on available estimates of species' sensitivity to these changes, and recombines them to create <1-km resolution maps of overall species vulnerability and threat-specific habitat vulnerability. To demonstrate its potential to guide decision-making, we applied this approach to the Gunnison sage-grouse (Centrocercus minimus), a federally threatened habitat specialist that depends on sagebrush and mesic habitats that are imperiled by climate change. We mapped six threats forecasted out to the year 2070: direct effects of climate on (1) sagebrush cover loss and (2) mesic habitat drying, indirect changes in invasion risk from (3) pinyon–juniper conifers and (4) annual grasses, and potentially synergistic risk of (5) development and (6) wildfire. We then assessed species vulnerability for each of the eight extant populations under three climate scenarios: Optimistic, Continuation, and Pessimistic. We found that the extent of cumulative species vulnerability due to multiple habitat changes was far greater than the extent of any single habitat vulnerability. Over 75% of critical habitats were at risk under the Pessimistic scenario, and nearly two thirds of habitats were at high risk for three or more threats. Invasive species were the most widespread threat, highlighting the importance of indirect effects of climate change. We illustrate how our approach can be applied to the existing management planning strategies to better prioritize conservation of habitats for the persistence of threatened species.