Micronutrient deficiencies (Fe, Zn, Cu, Mn, B, and Mo) in food crops are primarily driven by high soil pH and contribute to hidden hunger. Alternatively, micronutrient nano-fertilizers could serve as promising nanomaterials for the efficient delivery of micronutrients to plants when compared with traditional fertilizers. In-depth details are provided on different types of micronutrient nano-fertilizers (nanoparticles, nanochelates, and nanocapsules), including their synthesis, characterization, and potential agricultural applications. Particular emphasis has been placed on how such formulations can affect plant growth, productivity, and stress resilience. Finally, insights into the possible adverse effects of nano-micronutrients on growth and physio-biochemical traits have been provided, indicating their potential for future applications and integration with traditional agricultural practices. In the future, these nano-micronutrients could serve as excellent candidates for biofortifying crops.