Integrated management of coral reef foods, as a highly diverse set of blue foods, can contribute to addressing the dual challenges of malnutrition and biodiversity loss. Advances in nutrition research have made it possible to understand nutritional benefits on a species by species basis, and to make comparisons with benefits derived from land-based foods. We provide a series of considerations about current understanding of nutrition from coral reef foods, including the predominance of finfish in nutritional assessments, the importance of contaminants for food safety, uncertainty stemming from climate and cumulative impacts, and the need for locally specific assessments of food systems. Next we outline how nutrition, coral reef small-scale fisheries, and communities intersect. Aspects of equity and food sovereignty are reviewed as a basis for contextualizing current scientific understanding of nutrition while acknowledging who is actually benefiting nutritionally and materially from coral reef fisheries. Given this understanding of the state of knowledge of nutrition from coral reef foods, we encourage the development of nutrition-sensitive coral reef governance. We conclude with a set of recommendations for governance institutions, fishing organizations, philanthropic foundations, funding agencies, conservation organizations, and researchers, among others.