World leaders have committed to the 2020 goal under the Convention on Biological Diversity to improve the status of biodiversity. A suite of biodiversity indicators is currently used to monitor progress towards achieving these targets. Several indicators exist for measuring loss of species diversity and abundance, yet comprehensive indicators measuring change across ecosystems globally are lacking. We fill this gap by developing biodiversity indicators for ecosystems based on the data from the International Union for the Conservation of Nature’s Red List of Ecosystems (RLE), the global standard for assessing the risks to ecosystems. Our indicators quantify spatial and temporal changes in risk status, area, and health of ecosystems across all biomes over recent, future and historical timeframes, using the Red List Index and Living Planet Index as models. Using the RLE biodiversity indicators, we quantify: (i) the overall risk of ecosystem collapse globally; and (ii) the proportional change in the area of the ecosystem and loss of ecosystem health to show progress through time towards ecosystem collapse (i.e. ecosystem endpoint). The RLE biodiversity indicators allow spatial comparisons of the relative risk of collapse and the type of change occurring among ecosystems from local to global scales. Our indicators synthesise complex information to highlight regions most at risk of collapse, and allow clear communication with decision-makers, managers and the general public. This information will inform progress towards the 2020 Aichi targets for the Convention of Biological Diversity, and the UN Sustainable Development Goals, and guide future policy and management prioritization.