AbstractOcean warming is already causing widespread changes to coral reef ecosystems worldwide. Warming is having direct and indirect impacts on food webs, but their interaction is unclear. Warming directly affects fishes and invertebrates by increasing their metabolic rate, resulting in changes to demographic processes such as growth rates. Indirect effects involve a loss of reef habitat quality as coral bleaching reduces the availability of refuges. We used a size‐structured dynamic energy budget model of fishes and invertebrates, coupled to a spatially explicit model of coral and algae, to explore potential changes to ecosystem function with warming. Modeled changes in biomass for +3°C of warming were found to be controlled predominantly by the direct effects of warming on growth rates, rather than by indirect effects via the changed coral habitat. Crucially for fisheries, the biomass of predators decreased by at least 50% with +3°C of warming, and productivity of predators decreased by at least 60%.