Microgreens, also known as “functional greens” or “vegetable confetti,” are tender, nutrient-rich seedlings harvested at the first true leaf stage. Rich in vitamins, minerals, antioxidants, and phytochemicals, they are a powerful addition to a healthy diet. To enhance their nutritional profile, biofortification strategies such as agronomic enrichment and nanotechnology offer a promising approach to boost their micronutrient content and combat hidden hunger. Notable differences in nutrient content, such as vitamin C, carotenoids, and essential minerals across species and genotypes were identified. Breeding programs focusing on the development of nutrient-rich microgreen varieties and hybrids play a crucial role in improving their functional value. Traditional methods like selection and hybridization continue to be effective in utilizing genetic diversity to enhance key traits such as yield, flavor, and nutritional quality. The incorporation of advanced techniques including genomics-assisted breeding, metabolomics, transcriptomics and speed breeding has further accelerated the improvement of nutritional and functional traits in microgreens. Therefore, the integration of conventional and molecular approaches enables the efficient development of superior microgreen cultivars with enhanced agronomic and nutritional performance. Looking forward, cutting-edge tools such as CRISPR/Cas genome editing hold immense potential for precise trait improvement, opening new avenues for next-generation microgreens with tailored health benefits. This chapter thus explores the genetic and molecular strategies driving the enhancement of microgreens for high-quality and health-promoting produce.