It is known that coral reefs were absent in the central Indo-Pacific during the Early Pliocene. This study uses a new temperature record based on TEX₈₆^H biomarkers from the Coral Sea between 11–2 Ma to show a 2 °C cooling in the central Indo-Pacific during the Late Miocene Cooling (7–5.4 Ma). This cooling triggered changes in terrestrial input, ocean circulation, and temperature. These multiple stressors could have caused reef collapses across the central Indo-Pacific.