<p>The biosynthesis of nanoparticles (NPs), using microbial extracellular metabolites, represents an eco-friendly alternative to conventional physical and chemical methods for NP synthesis. Microorganisms release diverse metabolites, including redox-active compounds, extracellular polymeric substances (EPS), and biosurfactants, which facilitate the reduction and stabilization of NPs. Recent advancements in bioinformatics have transformed microbial NP synthesis by enabling metabolic pathway analysis, molecular docking, and genome mining. This review highlights the bioinformatics-driven role of microbial extracellular metabolites in NP synthesis and stabilization. Computational tools such as machine learning models, PRISM, and antiSMASH were employed for docking studies between metabolites and metal ion precursors to elucidate the mechanisms of NP synthesis. Molecular docking results revealed that key extracellular metabolites such as NADH reductase, surfactin, curdlan synthase, and pullulanase effectively interact with metal ion precursors such as silver, zinc, and iron ions, subsequently reducing them into respective NPs and stabilizing them. Furthermore, SwissADME-based bioinformatics analysis assessed hydrophilicity, lipophilicity, and hydrogen bonding potential, confirming NADH as a potent reducing agent, while surfactin and pullulanase functioned as capping and stabilizing agents. The study also discusses the effects of parameters such as pH, temperature, and reactant concentration on the NP synthesis and stabilization process, along with the advanced applications of such NPs. However, limitations related to scalability, insufficient characterization techniques, and variability in microbial metabolite production hinder their widespread application. Future research should focus on integrating synthetic biology, bioinformatics, and nanotechnology to improve the efficiency of nanoparticle biosynthesis.</p>