The rising global population and widespread deficiencies in micronutrients pose ongoing challenges to the quantity and quality of food security, exacerbating issues of malnutrition and associated health concerns termed “hidden hunger,” notably in developing nations. Despite considerable efforts in the agriculture sector to enhance nutrient content in cereals, successes have been insufficient to reduce malnutrition significantly. Legumes, integral to the food systems in sub-Saharan Africa and South Asia, have seen limited efforts to enhance their nutrient content. However, the germplasm pool of legume crops has genetic variation for a wide range of nutritional properties, which can be used to improve the nutrient content of seeds by selective breeding. The targeted identification and utilization of precise nutritional traits in breeding programs can help mitigate malnutrition. Several challenges, including the intricate balance between yield and protein content, the interplay of various micronutrients, and the need to reduce anti-nutritional factors, hinder the nutritional enhancement of legumes. Conventional breeding methods, while effective, could be faster and improved by limited genetic variation. However, modern plant breeding tools offer promising solutions. Genetic engineering, marker-assisted selection (MAS), and genome editing enable precise manipulation of plant genomes, accelerating breeding and expanding the pool of genetic resources. Advances in gene editing, such as CRISPR/Cas9 technology, offer novel avenues for improving nutritional content while addressing regulatory and consumer concerns. Integrating these modern breeding approaches is essential for developing bio-fortified legume crops. This chapter aims to understand the nutritional merit of legumes and the associated breeding techniques to breed nutritionally superior legumes, combining knowledge of conventional and modern breeding tools to develop micronutrient-dense, anti-nutrient-free varieties to address malnutrition and hidden hunger.