Climate change is causing ecoregions to shift in the Hindu Kush Himalayas, threatening both ecosystem services and biodiversity in the region. As these ecoregions shift, important ecological processes may be disrupted and species ranges may begin to move outside the protected areas that were designed to conserve them. Although transboundary landscape initiatives and adaptive management strategies exist in the HKH to mitigate these negative impacts, researchers and practitioners need methods to project how ecoregions may shift in response to the evolving conditions of climate change. Zomer et al. (2014) present one such method, whereby projected climate data is used to predict ecoregion distributions based on an environmental stratification method. Here, we adapt this approach to help address the priority knowledge gap identified by the Lima Adaptation Knowledge Initiative of the United Nations Framework Convention on Climate Change on the lack of methodologies and tools to quantify the impact of climate change on ecosystem services, biodiversity, and forests in HKH subregion. We accomplish this aim by a) modeling ecoregion shifts in the transboundary Kangchenjunga Landscape of the HKH under two Shared Socioeconomic Pathway projected climate scenarios, b) increasing the transparency, replicability, and accessibility of the modeling process by providing shareable code, and c) examining how these projected ecoregion shifts may impact biodiversity and ecosystem services in HKH protected areas. Our model found that by the year 2100, high-elevation ecoregions (3,000m - 8,586m) will either shrink or shift to higher elevations, mid-elevation ecoregions (500m - 3,000m) will expand, and low-elevation ecoregions (0m - 500m) will shrink substantially. We assess how shifting ecoregions may impact the ability of protected areas to conserve umbrella species (i.e., snow leopard, red panda, Asian elephant, tiger) and ecosystem services as exemplified by the Rhododendron genus. Researchers, academics, and practitioners can iterate, expand, and modify this method to inform management plans that protect species, people, and ecosystems from the threat of climate change.