Abstract The Mt Elgon ecosystem straddles the international boundary between Kenya and Uganda and is a watershed of international importance, feeding the waters of Lake Victoria, the Nile River system, and Lake Turkana. The core ecosystem in the Mt Elgon area is characterized by large montane forest landscapes; it comprises several protected areas. Adjacent is a vast, heavily populated agricultural landscape supporting up to 2 million people, whose livelihoods and economic activities are largely dependent on the ecosystem goods and services of the highlands. The mountain ecosystem of Mt Elgon is thus vital to the social and economic functioning of the surrounding areas, both in the highlands and in the lowlands. To manage this important ecosystem and sustain the multiple functions and services it offers local people and visitors, there is a need for a regional transboundary ecosystem management approach and strengthened institutional collaboration between all stakeholders concerned at different levels. The Mt Elgon Regional Ecosystem Conservation Programme (MERECP) aims to secure the multifunctionality of the Mt Elgon ecosystem and enhance sustainable development in the long term, in order to secure livelihoods and alleviate poverty, both of which are priorities of the governments of Uganda and Kenya. The present article provides insights from experience and lessons learned to date regarding the planning and implementation of such a transboundary regional ecosystem approach.