Malnutrition or hidden hunger due to micronutrient deficiencies (iron, zinc, vitamin A, iodine) affects over 2 billion people worldwide, with the greatest burden in developing countries. Biofortification, the practice of breeding staple food crops that are rich in specific micronutrients through agronomic, conventional or modern genetic approaches, is a cost-effective and sustainable approach to combat malnutrition at a population scale. This review paper covers recent developments in biofortification with special focus on developing nutrient-dense varieties using genomic tools, marker-assisted selection (MAS) and omics technologies, as well as microbial-assisted biofortification using plant growth-promoting rhizobacteria (PGPR) and mycorrhizal fungi (MF). Additionally, the paper identifies future research trajectories, including the potential biofortification of other underutilized crops such as millets and pulses (many of which are already naturally high in key micronutrients and adapted to harsh climates), digital agriculture, artificial intelligence and climate-resilient practices for greater efficiency and scale. Biofortification is a science-based strategy that holds great promise for achieving nutrition goals globally, but its success will rely on interdisciplinary collaboration, policy support and stakeholder engagement within the agriculture, health and education sectors. Prospective directions for further research include exploring multi-nutrient biofortification, integrating biofortification with sustainable soil–plant–microbe interactions and leveraging systems biology to optimize nutrient uptake and stability. Future challenges involve ensuring consumer acceptance, addressing bioavailability issues, minimizing trade-offs with yield and quality and strengthening policy frameworks to enable large-scale adoption and equitable access.