Biodiversity is declining at an unprecedented rate with infrastructure development being one of the leading causes. New infrastructure, such as roads, provides new access and results in increased land clearing and wildlife hunting. A number of large infrastructure projects, including new roads and rail, are being planned in Nepal. We show the application of readily available remotely sensed data and geospatial tools to assess the potential impact of these future developments on habitat quality under three protection-level scenarios. Our findings reveal that there is currently large spatial heterogeneity in habitat quality across the landscape as a result of current anthropogenic threats, and that three areas in particular could have up to 40% reduction in habitat quality as a result of the planned infrastructure. Further research is required to determine more precisely the impact on key species. Strengthening protected areas and buffer zones will contribute to mitigating degradation to some degree, however, large areas of biologically significant areas outside protected areas will be affected without new controls. Our geographic information systems (GIS) based methodology could be used to conduct studies in data poor developing countries, where rapid infrastructure development across ecological sites are ongoing, in order to make society, policy makers, and development planners aware.