Micronutrients are essential factors for human health and integral for plant growth and development. Among the micronutrients, zinc (Zn) and iron (Fe) deficiency in dietary food are associated with malnutrition symptoms (hidden hunger), which can be overcome through biofortification. Different strategies, such as traditional and molecular plant breeding or application of chemical supplements along with fertilizers, have been employed to develop biofortified crop varieties with enhanced bioavailability of micronutrients. The use of microorganisms to help the crop plant in more efficient and effective uptake and translocation of Zn and Fe is a promising option that needs to be effectively integrated into agronomic or breeding approaches. However, this is less documented and forms the subject of our review. The major findings related to the mobilization of micronutrients by microorganisms highlighted the significance of (1) acidification of rhizospheric soil and (2) stimulation of secretion of phenolics. Plantmicrobe interaction studies illustrated novel inferences related to the (3) modifications in the root morphology and architecture, (4) reduction of phytic acid in food grains, and (5) upregulation of Zn/Fe transporters. For the biofortification of Zn and Fe, formulation(s) of such microbes (bacteria or fungi) can be explored as seed priming or soil dressing options. Using the modern tools of transcriptomics, metaproteomics, and genomics, the genes/proteins involved in their translocation within the plants of major crops can be identified and engineered for improving the efficacy of plant-microbe interactions. With micronutrient nutrition being of global concern, it is imperative that the synergies of scientists, policy makers, and educationists focus toward developing multipronged approaches that are environmentally sustainable, and integrating such microbial options into the mainframe of integrated farming practices in agriculture. This can lead to better quality and yields of produce, and innovative approaches in food processing can deliver cost-effective nutritious food for the undernourished populations.