Small-scale fisheries provide nutrients to hundreds of millions of people worldwide, with yields dependent on the condition of marine habitats such as coral reefs. Small-scale fisheries are a particularly important food source in societies with nutrient deficiencies and where unhealthy food alternatives are widely available. Using data from coral reef surveys around two islands in French Polynesia (Moorea and Raiatea), we show how the availability of nutrients to fisheries changed in relation to the condition of coral habitat. Fish biomass and nutrient availability were highest when coral cover was low around both islands, driven predominantly by abundant herbivorous reef fish. We also investigated the importance of fish in people’s diets, to determine if fish consumption was aligned with available fisheries resources on local reefs and if nutrient intakes from fish could be explained by people’s socioeconomic background. People ate a higher diversity of reef fish in Raiatea, however nutrient intakes from fish were higher in Moorea. Most people ate more fish than meat on both islands, however fish consumption declined over generations. People from fishing households had higher nutrient intakes from reef and pelagic fish, and people from farming households had higher intakes from reef fish. Preference for eating reef fish over pelagic fish was also associated with higher total nutrient intakes. Promoting traditional diets rich in fish could be key to meeting people’s nutritional needs in French Polynesia while reducing diet-related health issues linked to the overconsumption of fat. French and Tahitian versions of the Abstract are available in Supplementary Material.