Highlights
• Multi-omics analysis revealed the improving mechanism of Monascus bioaugmentation in rosy vinegar.
• Monascus rice (MR) promoted the proliferation of Rhizopus and Acetobacter in two stages.
• Amount of amino acid nitrogen, organic acids and FAAs raised in MR vinegar.
• Antioxidant capacity and bioactive metabolites notably enhanced in Jinhua-MR vinegar.
• Starch and sucrose metabolism was the most significantly enriched pathway in Jinhua-MR.

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