Anairetes alpinus is currently categorized as an endangered species due to range fragmentation and habitat loss across its geographic distribution. Its range is only partially known, and potential effects of future climate change on its distribution have yet to be assessed. Using ecological niche models and future climates information, we assessed the geographic and environmental potential distribution of A. alpinus for the years 2050 and 2070, analyzing effects of habitat loss and the importance of existing protected areas (PAs) across the species’ range. Our ecological niche models predicted a distributional range of ~ 59,000 to ~ 64,400 km2 for the species, extending from northern Peru to northern Bolivia. However, habitat loss led to an important reduction (> 57%) in the current potential suitable areas. On average, the climate change reduced the potential distributional areas by ~ 49% and ~ 61% for 2050 and 2070, respectively. Synergistic effects of climate change and habitat loss are predicted to pose an even greater risk, leading to a net reduction in future potential distributions of over 75%. We also observed a shift of ~ 230 m increase in elevation between the range under present conditions and scenarios for 2050 and 2070. Although PAs were more suitable climatically than surrounding areas, for future scenarios, we observed an important reduction (on average over 25%) of proportion of PAs within the estimated distributional areas, as well as a significant (P < 0.05) reduction in mean habitat suitability values within PAs. Our novel results offer a guide for future integrative studies focused on defining conservation units and ecological corridors across the distribution of many Andean species.