Coral bleaching events, caused by cumulative thermal stress during marine heatwaves, are rapidly restructuring coral reef communities. The severe global heatwave of 2016 was no exception, causing mass coral bleaching and large changes in reef fish communities. While the effects of coral bleaching on community assemblages has been quantified at local to regional scales, their effects on the functional diversity of reef fish has not yet been investigated at broad spatial scales. Using Reef Life Survey data from before and after the 2016 marine heatwave, and Bayesian joint species distribution models, we quantified changes in community trait composition for 200 fish species along thermal stress gradients at a continental scale. We find that cumulative heat stress, measured as degree heating weeks, had the strongest effect on the species-level responses and magnitude of predicted functional change – with distinct functional communities displaying the same direction of change across all traits. Our modelling suggests that human induced climate change, and associated increases in marine heatwave frequency and severity, will drastically alter the trait assemblage of coral reef fish communities, curtailing functional richness. This has critical implications for coral reef health and the vital ecosystem services they provide to nature and people.