Safe and nutritious foods are a requisite for achieving food security. Urbanization and dietary shifts have made food value chains more complex, affecting food safety and nutrient loss. Preventing food quality loss (FQL) requires understanding the impact of market incentives, value chain capacity, and governance on FQL pathways. Food hazards, such as biological, chemical, and physical contaminants, can be introduced at any stage of the food value chain. Understanding the sources of hazards, high-risk foods, and transmission pathways is essential for effective FQL prevention. Nutrient loss occurs throughout the food value chain, from harvest to consumption. Factors influencing nutrient loss include processing methods, storage conditions, handling practices, and the specific attributes of the food itself. FQL pathways involving nutrient loss are particularly concerning when essential micronutrients are depleted from foods, which are considered primary dietary sources of those nutrients. By considering specific food system contexts and trade-offs between food safety and nutrient loss, governments can implement effective approaches to reduce FQL and deliver healthy diets.