Ecosystems worldwide are under increasing threat. We applied a standardized method for assessing the risk of ecosystem collapse, the International Union for Conservation of Nature (IUCN) Red List of Ecosystems, to coral reefs in the Western Indian Ocean (WIO), covering 11,919 km2 of reef (~5% of the global total). Our approach combined indicators of change in historic ecosystem extent, ecosystem functioning (hard corals, fleshy algae, herbivores and piscivores) and projected sea temperature warming. We show that WIO coral reefs are vulnerable to collapse at the regional level, while in 11 nested ecoregions they range from critically endangered (islands, driven by future warming) to vulnerable (continental coast and northern Seychelles, driven principally by fishing pressure). Responses to avoid coral reef collapse must include ecosystem-based management of reefs and adjacent systems combined with mitigating and adapting to climate change. Our approach can be replicated across coral reefs globally to help countries and other actors meet conservation and sustainability targets set under multiple global conventions—including the Convention on Biological Diversity’s post-2020 global biodiversity framework and the United Nations’ Sustainable Development Goals.