Climate change affects ecosystems globally, but their diversity and complexity make it difficult to estimate how severe these impacts are. Here we discuss how to conceptualize the effects of climate change on ecosystems so that they can be reliably captured in ecosystem risk assessments, focusing on the International Union for Conservation of Nature Red List of Ecosystems, a headline indicator for the Kunming-Montreal Global Biodiversity Framework. We highlight key challenges and propose solutions, which include using diverse teams, conceptual models and data sources (including projections), learning from analogous ecosystems, and evaluating uncertainties. This approach will improve the capacity to produce reliable assessments of risk under climate change to inform timely and effective conservation.