Malnutrition is a multidimensional issue, spanning at its heart both the quantity and quality of food. In recognition of the trade-off between yields and micronutrient quantity, biofortified and engineered crops have been developed. However, restrictive genetically modified organisms GMO legislation, shifting climate challenges, and public opposition have questioned their utility in the food chain. With the rise of synthetic biology, an alternate paradigm is developing whereby the production of traditional plant natural products and micronutrients are being explored using microorganisms, with the view of micronutrient supplementation and the development of functional food products. It is envisaged that successful implementation of metabolic engineering, data analytics, and synthetic biology of microbial micronutrient and food production systems will play a significant role in shaping the future of food production, food economics, farming, and human nutrition. Decreasing level of micronutrients in cereal crops is a serious issue, and this hidden hunger will be addressed by the developments in synthetic biology driven microbial production platforms in the future.