Micronutrients are defined as substances in foods that are essential for human health and are required in small amounts. They include all of the known vitamins and essential trace minerals. Micronutrient malnutrition affects a third to a half of the global population. It causes untold human suffering and levies huge costs on society in terms of unrealized human potential and lost economic productivity. The goal of this paper is to identify deficiencies in the food system that lead to micronutrient malnutrition and explore and evaluate strategies for its prevention. We examine the impact of agricultural practices on micronutrients in the food supply, including cropping systems, soil fertility and animal agriculture. We then discuss the potential of biofortification –i.e. increasing the concentration of micronutrients in staple food crops through conventional plant breeding or genetic engineering– as a means to reduce micronutrient deficiency. In addition, we discuss the impact of food losses and food waste on micronutrients in the food supply, and we explore successful strategies to preserve micronutrients from farm to plate, including food fortification. Our review of the literature sheds light on the advantages and limitations of alternative interventions to reduce micronutrient deficiencies along the supply chain. We end with recommendations for actions that will reduce the prevalence of micronutrient malnutrition.