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Compared with traditional carbon sources such as glucose, glycerol enhances the production of various secondary metabolites such as aromatic compounds, polyols, and lipids in microorganisms such as <jats:italic>Komagataella phaffii<\/jats:italic> and <jats:italic>Yarrowia lipolytica<\/jats:italic>. For instance, in <jats:italic>K. phaffii<\/jats:italic>, glycerol increased the titers of <jats:italic>p<\/jats:italic>-coumarate, naringenin, and resveratrol compared with glucose-based media, particularly when combined with specific amino acid supplementation. This review presents recent advancements in the production of secondary metabolites from glycerol. The metabolic pathways involved in glycerol utilization and secondary metabolite biosynthesis have been examined with insights into the regulation of these processes. The potential applications of glycerol-derived secondary metabolites in the pharmaceutical, food, and biofuel industries have been discussed. Finally, the challenges such as strain robustness, variability in crude glycerol quality, and downstream processing have been addressed with focus on recent innovations in metabolic engineering, redox tuning, and bioprocess control. Overall, this review highlights the potential of glycerol in the context of these advancements as a sustainable and cost-effective feedstock for the next-generation microbial biomanufacturing of high-value secondary metabolites.<\/jats:p>\n          <jats:p>\n            <jats:bold>Graphical abstract<\/jats:bold>\n          <\/jats:p>","DOI":"10.1007\/s11274-025-04537-x","type":"journal-article","created":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T03:45:40Z","timestamp":1757907940000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Harnessing glycerol for secondary metabolite biosynthesis in microorganisms"],"prefix":"10.1007","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-2900-7951","authenticated-orcid":false,"given":"Kouhei","family":"Kamasaka","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz","family":"Marcello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1089-7627","authenticated-orcid":false,"given":"Luc\u00edlia","family":"Domingues","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8382-2362","authenticated-orcid":false,"given":"Tomohisa","family":"Hasunuma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,9,15]]},"reference":[{"key":"4537_CR1","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13068-019-1597-2","volume":"12","author":"MR A\u00dfkamp","year":"2019","unstructured":"A\u00dfkamp MR, Klein M, Nevoigt E (2019) Saccharomyces cerevisiae exhibiting a modified route for uptake and catabolism of glycerol forms significant amounts of ethanol from this carbon source considered as non-fermentable. 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