As one of the global biodiversity hotspots, the mountains of Central Asia are home to a large number of wild fruit species. Although the hotspots are constantly being seriously affected by climate and land-use changes, effective assessments of the impacts of these changes for the dominant species of wild fruit forests, wild apple (Malus sieversii), have been limited. We compiled 8344 occurrence records for wild apple across its whole distribution ranges from field surveys and herbarium and literature records. After data thinning to reduce sampling bias, we used ensemble niche models to project current and future suitable habitats, examined the importance of environmental factors, and assessed whether current national protected areas (PAs) are effective in protecting the suitable habitats. We found that the distribution of wild apple is currently fragmented. Under future scenarios, it would shift 118–227 km towards high latitudes and ~200 m towards high elevations, losing nearly 27–56% of suitable habitats in the south, and gaining some habitats in the north. The increased temperature and expansion of cropland contributed to these shifts. Nevertheless, about 13% of the suitable habitats are covered by existing PAs and less than 25% of suitable habitats will be protected in the future. The cold spots for protecting intact wild fruit forests are located in Xinjiang, China and Kyrgyzstan. Overall, we provide a detailed evaluation of the impacts of climate and land-use changes on current and future distributions of wild apple in Central Asia. Considering that this species faces a greater risk of habitat loss in the south of Central Asia, we advocate developing effective in situ conservation strategies with long-term monitoring that will provide deep insights into the fate of wild fruit forests.