Energy acquisition and nutrient recycling are key to the ecology, population dynamics, and stress resilience of every organism. These processes are especially important for reef-building corals as these organisms often live in nutrient-depleted water. The coral’s energy budget depends on (i) the metabolites and nutrients derived from the vast diversity of microorganisms they harbour and (ii) direct heterotrophic feeding, which relies on processes occurring in the water column. Here we provide an overview of the nutrient cycling mediated by microorganisms across multiple scales in coral reefs to better characterise the multifaceted aspects of coral nutrition allowing them to thrive in nutrient deserts. We first consider how corals influence nutrient cycling in reef waters and sediments. We then focus on the microbially-mediated chemical transformations taking place in different coral micro-environments, as they are key to the recycling of nutrients and the de novo production of molecules essential to coral health. Finally, we describe how the direct capture of prey and particulate matter from reef waters contributes to the energy budget and stress tolerance of corals.