Climate change, rapid urbanization, war, and economic recession are key drivers of the current food systems’ disruption, which has been exacerbated by the COVID pandemic. Local, regional, and global food systems are unable to provide consumers with nutritious and affordable diets. Suboptimal diets exacerbate the triple burden of malnutrition, with micronutrient deficiencies affecting more than two billion people, two billion people suffering from overweight, and more than 140 million children who are stunted. The unaffordability of nutritious diets represents an obstacle for many, especially in low- and middle-income countries where healthy diets are five times more expensive than starchy staple diets. Food system transformations are urgently required to provide consumers with more affordable and nutritious diets that are capable of meeting social and environmental challenges. In this review, we underline the critical role of innovation within the food system transformation discourse. We aim to define principles for implementing evidence-based and long-term food system innovations that are economically, socially, and environmentally sustainable and, above all, aimed at improving diets and public health. We begin by defining and describing the role of innovation in the transformation of food systems and uncover the major barriers to implementing these innovations. Lastly, we explore case studies that demonstrate successful innovations for healthier diets.