Future climate change will result in profound shifts in the distribution and abundance of biodiversity in the Tropical Andes, and poses a challenge to contemporary conservation planning in the region. However, currently it is not well understood where the impacts of climate disruption will be most severe and how conservation policy should respond. This study examines climate change impacts in the Peruvian Andes, with a specific focus on tropical montane forest ecosystems, which are particularly susceptible to climate change. Using an ensemble of classification models coupled with different climate change scenarios, we estimate high and low potential impacts on montane forest, by projecting which areas will become climatically unsuitable to support montane forest ecosystems by 2070. These projections are subsequently used to examine potential impacts on protected areas containing montane forest. The modeling output indicates that climate change will have a high potential impact on 58% of all montane forests, particularly in the elevation range between 800 and 1200 m.a.s.l. Furthermore, about 64% of montane forests located in protected areas will be exposed to high potential impact. These results highlight the need for Peru’s conservation institutions to incorporate climate change considerations into prevailing conservation plans and adaptation strategies. To adjust to climate change, the adaptive capacity of forest ecosystems in the Peruvian Andes should be enhanced through restorative and preventive conservation measures such as improving forest functions and mitigating deforestation and forest degradation pressures.