Climate change is transforming coral reef structures, with important yet largely unknown consequences for reef food webs. Crustaceans, molluscs, polychaetes, and other small motile invertebrates living as epifauna on coral habitats represent an essential trophic link between primary producers and a diverse and abundant invertivorous fish fauna. Here, we investigate variation in assemblages of motile epifaunal invertebrates on live coral and dead coral heavily overgrown by turf algae. Sampling was conducted 2–3 years following mass bleaching within the study region at four locations broadly spanning the distribution of corals on the eastern seaboard of Australia—along the northern and central Great Barrier Reef, and, adjacent to the central east coast, the Solitary Islands and offshore Elizabeth and Middleton Reefs (> 2000 km total distance). Epifaunal assemblages differed significantly between live and dead ‘turf-covered’ coral habitats, with overall density, biomass, and productivity of epifauna more than an order of magnitude greater on dead than on live coral. The size structure and composition of assemblages also differed: turf-covered dead coral supported greater abundances of small animals than live coral, notably harpacticoid copepods, while live coral assemblages had proportionally greater abundances of larger decapods. A ten-fold increase in secondary productivity of motile invertebrates is predicted as live corals are replaced by turf-covered dead coral, however, this productivity will predominantly be available as small harpacticoid copepod prey (size range: 0.125–0.25 mm). Associated flow-on effects through reef food webs are likely, as changes to epifauna will directly affect invertivore communities, which in turn potentially influence larger carnivores and other functional groups.