Current development models are leading to unprecedented environmental challenges, chief amongst them, climate change. How to respond to these challenges are key research questions. Although they are global problems, their effects are felt locally, especially by the communities that traditionally base their livelihoods in those natural resources. The relevance of these problems at global level has driven different initiatives to increase public awareness and to put in practice measures to improve them. However, many good conservation and management practices are done at local level. Research is needed to better understand local capabilities and to encourage and support potential locally-owned solutions. COMET-LA’s objective is to identify sustainable community-based governance models for the management of natural resources that could be used in different social-ecological systems in a context of climate change and increasing competition for the use of these resources. A civil society-scientific partnership has been created to develop the project. Three Latin American civil society organizations, a global CSO and 7 research institutions (3 Latin American and 4 European) comprise this partnership. COMET-LA will create a space of interaction for CSOs, policy makers and research organizations, sharing local and scientific knowledge and contributing to a better knowledge of problems and potential solutions for current and future sustainable management of natural resources. Three different case studies will be analyzed: water and biodiversity systems in Colombia, forest systems in Mexico and marine and coastal areas in Argentina. Similar methods will be used to characterize the current and future ecosystem states, sustainable governance models and locally-tailored scenarios for future changes and challenges. The outcomes will be synthesized and up-scaled to deliver a potentially useful tool to other local communities facing current environmental challenges.