Coral reefs are in global decline. Reversing this trend is a primary management objective but doing so depends on understanding what keeps reefs in desirable states (ie “functional”). Although there is evidence that coral reefs thrive under certain conditions (eg moderate water temperatures, limited fishing pressure), the dynamic processes that promote ecosystem functioning and its internal drivers (ie community structure) are poorly defined and explored. Specifically, despite decades of research suggesting a positive relationship between biodiversity and ecosystem functioning across biomes, few studies have explored this relationship in coral reef systems. We propose a practical definition of coral reef functioning, centered on eight complementary ecological processes: calcium carbonate production and bioerosion, primary production and herbivory, secondary production and predation, and nutrient uptake and release. Connecting research on species niches, functional diversity of communities, and rates of the eight key processes can provide a novel, quantitative understanding of reef functioning and its dependence on coral reef communities that will chart the transition of coral reefs in the Anthropocene. This will contribute urgently needed guidance for the management of these important ecosystems.