Payment for Ecosystem Services (PES) can promote different types of governance arrangements to address the triple challenge of biodiversity loss, climate change and air pollution. These institutional arrangements, however, do not explicitly incorporate climate change into the ecosystem's capacity to provide services. In this study, we explore why and how to incorporate climate uncertainties using as example the Altos de Cantillana Nature Reserve, a unique biodiversity hotspot in Central Chile. First, prioritized ecosystem services (ES) were grouped in bundles and linked to measured and modeled impacts of climate change on key water-related processes. Second, institutional barriers to PES were identified from case studies and analyzed considering challenges in a changing climate. Finally, bundles with different levels of risk were matched to six recommendations that better incorporate levels of risks to the uncertainty of climate change into Payment for Ecosystem Services in Chile.