Abstract Although Citri Reticulatae Pericarpium (CRP) extracts can enhance cigar tobacco leaf (CTL) quality, the specific contributions of CRP-associated microbiota to CTL quality remain unexplored. This study investigated the potential of Bacillus cereus C3X-5, a strain isolated from CRP, as a bio-enhancer for improving CTL fermentation quality. The physicochemical analysis, metagenomics, and untargeted metabolomics were employed to systematically evaluate the strain’s impact.