Microbial-assisted biofortification emerges as a promising, sustainable alternative, leveraging the symbiotic relationships between plants and soil microorganisms to enhance selenium uptake and accumulation. This review critically assesses the advancements and perspectives in microbial biofortification of plants with selenium, a process vital for addressing the widespread selenium deficiency affecting human and animal health. The review utilizes a systematic literature review approach adhering to the PRISMA methodology, employing databases such as Scopus and Web of Science. Advanced methodologies including evidence mapping, data synthesis, research weaving, and Latent Dirichlet Allocation (LDA) for topic modeling, provide a comprehensive and nuanced understanding of the field. The primary focus is on the role of various microorganisms, particularly arbuscular mycorrhizal fungi (AMF), plant growth-promoting fungi (PGPF), rhizobacteria (PGPR), and microbial consortia, in the selenium biofortification process. Results indicate significant gaps in the current research, especially in exploring the potential of PGPF, PGPR, and microbial consortia. The study highlights the predominance of research on AMF, particularly Glomus species, while noting a lack of comprehensive evaluation of the selenium reduction and nanoparticle synthesis capabilities of other beneficial microbes. Additionally, the absence of standardized methodologies for assessing biofortification efficiency complicates cross-study comparisons, underscoring the need for uniform evaluation protocols. The analysis reveals that while microbial transformations of selenium, such as the reduction to elemental selenium nanoparticles (SeNPs), are well-documented, the practical application of SeNPs for plant biofortification remains limited. Sustainable selenium sources, like agro-industrial wastes, are underexplored compared to traditional selenium sources such as selenium salts and seleniferous soils.