BACKGROUNDPolyphenolic compounds in millet vinegar are crucial functional substances, but the mechanisms underlying their formation and metabolism remain unclear. Acetic acid fermentation (AAF) represents the most active microbial metabolism stage and is pivotal for forming polyphenolic compounds. This study comprehensively analyzed the role of the microbiome in polyphenolic compound production and metabolism during AAF.RESULTSChanging patterns were observed in both the microbiome and polyphenolic monomer compounds during AAF of millet vinegar. Lactobacillus harbinensis (0.624–0.454%) was identified as the dominant species in the pre‐AAF stage, exhibiting a significant positive correlation with caffeic acid, kaempferic acid and kaempferolide (P < 0.05). Lactobacillus harbinensis‐mediated polyphenolic compound metabolism was further confirmed through genomic analysis and pure culture fermentation techniques. Lactobacillus harbinensis encodes enzymes such as carbohydrate hydrolases, glycosidases and cellulases, which promote the release and metabolism of polyphenolic compounds from grain hulls.CONCLUSIONThis study confirmed that L. harbinensis, as a core microorganism in millet vinegar fermentation, can significantly augment the content of total phenols and specific polyphenolic compounds. These findings provide valuable insights for optimizing millet vinegar production. © 2024 Society of Chemical Industry.