Rice (Oryza sativa), is a cereal crop crucial for global food security. The limited availability of the micronutrients iron (Fe), manganese (Mn), and zinc (Zn) in calcareous soils can lead to metabolic disturbances in the plant, which are shown in several anomalies reducing yield and, in severe situations, the plant dead. These three micronutrients can be solubilized through plant growth-promoting microorganisms naturally found in the soil rhizosphere. These microorganisms have been also isolated from soils and used as biostimulants and biofertilizers, facilitating their use to optimize rice cultivation. This literature review describes the nature, assimilation, and significance of the micronutrients Fe, Mn, and Zn in the soil and in rice cultivation. It also investigates the use of more relevant microorganisms Bacillus, Pseudomonas, and Azospirillum as ingredients that promote rice growth and productivity. Furthermore, it discusses their mechanisms: the secretion of the siderophores deoxymugenic acid (DMA) and mugenic acid (MA); the production of organic acids like indole-3-acetic acid (IAA) and abscisic acid; the production of phytohormones (i.e. cytokinins); and a network of metalloproteins that facilitate soil acidification. These mechanisms enable the solubilization of Fe, Mn, and Zn in the soil associated with the crop, making them available for absorption by the root system in the form of chelates. In conclusion, Bacillus, Pseudomonas, and Azospirillum have the potential to enhance plant metabolic processes, alleviating micronutrient deficiencies and mitigating adverse environmental impacts.