The holistic approach has been applied to disaster risk evaluation at various scales, ranging from the urban to the national level, utilising deterministic and probabilistic physical risk results that concentrate on structures, infrastructure, and population effects. This article proposes a methodology to holistically evaluate the climate risk for ecosystems. Furthermore, the article proposes a prioritisation of adaptation measures based on their results, taking into account the physical risk, the ecological fragility conditions, and the strategic relevance of ecosystems exposed to these conditions. The calculation includes three composite indicators. The ecological fragility factor (FEF) estimates the capacity (or lack of capacity) of the ecosystem to absorb and recover, revealing vulnerabilities that may not be immediately evident but that can profoundly affect the long-term health and stability of the ecosystem. The ecosystem strategic relevance factor (FSR) helps to understand its fundamental role in supporting biodiversity and ecosystem services. The physical risk assessment does not account for the environmental and ecological aspects quantified through indicators in the FEF and FSR. A total risk index, RT, is calculated based on a probabilistic climate risk evaluation and the previously mentioned factors. This methodology is applied to the climate risk evaluation of Colombian ecosystems. The authors conducted this evaluation in close collaboration with Colombia's Ministry of Environment and Sustainable Development, funded by the Inter-American Development Bank. Its application yields crucial insights for informed decision-making and strategic planning in climate adaptation efforts.