Background <p>The dynamic role of selenium (Se) in soil–plant-microbe systems is critical for enhancing plant growth, improving stress tolerance, and promoting soil health.</p> Aims <p>This paper explores the mechanisms underlying Se transformation and bioavailability through interactions between soil microorganisms and plants. Microbial communities, including plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and phosphate-solubilizing bacteria, facilitate the reduction of Se oxyanions, converting them into elemental Se and organic forms. Key biogenic reductants such as glutathione, bacillithiol, hydrogen sulfide and siderophores are involved in Se reduction pathways. These transformations increase Se bioavailability, thus enhancing plant growth and modifying the rhizosphere microbial community structure, promoting beneficial microbial populations while suppressing harmful species. This review also addresses the potential of Se biofortification and its applications in improving agricultural productivity, as well as the role of Se in environmental remediation. Despite substantial progress in understanding Se transformation, the specific mechanisms, particularly related to Se transporters and reductases in both plants and microorganisms, require further exploration. The review identifies crucial areas for future research, including the optimization of Se biofortification strategies, the regulation of microbial communities, and the integration of Se into sustainable agricultural practices.</p>