Purpose <p>Biogenic selenium nanoparticles (SeNPs) offer an eco-friendly alternative to chemical synthesis for producing bioavailable and stable selenium. This study aimed to isolate an efficient Se(IV)-reducing bacterium from livestock manure and to elucidate the molecular mechanisms underlying SeNP biosynthesis, providing insight into its potential agricultural applications.</p> Methods <p>A selenium-transforming strain was isolated from goat manure and identified as <i>Lactiplantibacillus plantarum</i> SMB14 based on 16&#xa0;S rRNA sequencing. The strain was cultured in MRS broth supplemented with sodium selenite (Na₂SeO₃: 100&#xa0;mg L⁻¹) to produce SeNPs, which were characterized. Transcriptomic sequencing was conducted to compare gene expression profiles between control and Se(IV)-treated cells, and functional enrichment analyses were performed to identify metabolic pathways involved in Se(IV) reduction.</p> Results <p>SMB14 exhibited high Se(IV)-reducing efficiency (&gt; 80%) and produced extracellular SeNPs stabilized by biomolecular coatings. Transcriptome analysis revealed 978 differentially expressed genes, with significant upregulation of redox-active oxidoreductases (<i>qorB</i>, SDR family), thiol-related enzymes (<i>TrxA</i>, <i>GorA</i>), and membrane transporters (<i>pstS</i>, <i>glpF2</i>, <i>nhaC</i>). Functional pathways related to oxidative phosphorylation, amino acid metabolism, and cellular redox balance were significantly enriched, supporting a coordinated enzymatic–nonenzymatic reduction mechanism.</p> Conclusion <p>This study demonstrates that <i>L. plantarum</i> SMB14 employs a multi-pathway redox network to convert toxic Se(IV) into stable SeNPs through synergistic enzymatic and thiol-mediated reductions. These findings highlight the potential of SMB14 as a green biocatalyst for nanoselenium production and as a probiotic platform for sustainable selenium supplementation in agriculture and environmental biotechnology.</p>