In response to multiple stressors, coral reef health has declined in recent decades, with reefs exhibiting reduced living coral and structural complexity, and a concomitant rise in the dominance of algal resources. Reef degradation alters food availability and reduces the diversity and density of refuges for prey. These changes affect predator–prey interactions and can have cascading impacts on food webs and fisheries productivity. We use a size-based ecosystem model of coral reefs that incorporates the influence of structural complexity, benthic primary production and detrital recycling to explore how predator–prey interactions and fisheries productivity respond to a gradient of reef degradation. We show that fisheries productivity overall may be robust to initial stages of reef degradation because the benefits of increased resources outweigh the costs of moderate refuge decline. However, the assemblage composition and size structure of reef fish will differ on degraded reefs, with herbivores and invertivores contributing relatively more to productivity. More significant losses of refuges associated with the erosion of structural complexity correspond to fisheries productivity losses of at least 35% compared to healthy reefs. Synthesis and applications. Our model provides fisheries managers with quantitative predictions about how fisheries productivity may change in response to the ongoing degradation of coral reefs. We predict an initial increase in productivity at intermediate reef degradation, followed by a drastic decline when structural complexity is lost. We also capture subtle changes to potential catch composition and fish size, including increases in smaller herbivorous and invertivorous fish from degraded reefs, which will undoubtedly impact fisheries value. On the one hand, our results reassure for continued productivity in the short term, but on the other, we warn against complacency. Management must change to capture any potential benefits to fisheries, and long-term sustainability still depends on the maintenance of complex coral reef habitats.