There has been a serious health and environmental concern in conversion of inorganic mercury (Hg) to the neurotoxin, methylmercury (MeHg) by anaerobic microbes, while very little is known about the potential role of vitamin B9 (VB9) regulator in the biochemical generation of MeHg. This study innovatively investigated bacterial Hg methylation by Geobacter sulfurreducens PCA in the presence of VB9 under two existing scenarios. In the low-complexing scenario, the bacterial MeHg yield reached 68 % higher than that without VB9 within 72 h, which was attributed to free VB9-protected PCA cells relieving oxidative stress, as manifested by the increased expression of Hg methylation gene (hgcAB cluster by 19–48 %). The high-complexing scenario emphasized the intracellular Hg accumulation (38–45 %) after 12 h, as indicated by the increased expression of outer membrane protein-related and mercuric reductase-encoding genes, indicating the inefficient bioavailability of Hg due to a gradual shift from Hg reduction toward Hg0 re-oxidation controlled by competitive ligand exchange. These results suggested that VB9 application significantly raised the potential for bacterial Hg methylation and cellular accumulation, thus proposing insights into the biochemical behaviors of hazardous Hg in farming environments where vulnerable organisms are more possibly co-exposed to higher levels of Hg and VB9.