The planning and sustainable management of complex social-ecological systems (SESs) in high mountain areas such as the Hindu Kush–Karakoram–Himalaya (HKKH) region requires an approach that takes account of both environmental issues and local population needs. The HKKH Partnership Project developed methodologies and tools for systemic planning and management of social-ecological systems at local, regional, and national levels in the HKKH region, with a special focus on 3 protected areas in Nepal, Pakistan, and China. The adopted approach brought together researchers, policy-makers, and managers; it bridged the gap between research and management priorities and enabled communication to address the needs of communities while promoting conservation. Lessons learned are described and conclusions made on appropriate methods for the management of SESs in other regions.