Background <p>PpBMT encodes the bergaptol O-methyltransferase from the medicinal plant Peucedanum praeruptorum Dunn and belongs to the O-methyltransferase gene family. Although the role of O-methyltransferases (OMTs) in regulating drought stress responses through methylation of various secondary metabolites has been established in numerous plants, the physiological function of PpBMT remains poorly understood, particularly in heterologous systems. Notably, PpBMT has been characterized in vitro as highly specific for bergaptol. Whether it exhibits broader substrate recognition or exerts indirect metabolic effects when overexpressed in a heterologous system lacking the complete furanocoumarin biosynthetic pathway remains an open question.</p> Results <p>In this study, PpBMT was overexpressed in Arabidopsis, and drought tolerance was systematically compared with that of wild-type (WT) under PEG-induced drought stress. Under drought stress, transgenic lines showed a more sensitive phenotype than WT plants, with significant reductions in biomass, relative water content (RWC) and chlorophyll content. Their osmotic regulation and antioxidant defense systems were also severely impaired. Moreover, transgenic plants exhibited dysregulated expression of key drought-responsive genes, showing transient early hyperactivation followed by suppression. Notably, while transgenic plants accumulated higher concentrations of coumarins, including scopoletin, isoscopoletin, and isomarmesinin, under both normal and stress conditions, these compounds are structurally distinct from bergapten, the direct catalytic product of PpBMT, suggesting that the observed metabolic changes reflect broader network-level perturbations rather than direct enzymatic conversion.</p> Conclusions <p>Our results demonstrate that overexpression of PpBMT substantially altered coumarin metabolic flux in Arabidopsis and negatively regulated plant drought tolerance. This finding underscores that enhancing the accumulation of specific secondary metabolites does not necessarily confer improved stress resistance. Rather, the regulatory context, including stress-inducible, tissue-specific, and feedback-sensitive control of gene expression, is a critical determinant of physiological outcome. Although this study did not directly measure energy-related parameters or carbon allocation, and the sample size was modest, the dataset nevertheless provides valuable insights into the role of PpBMT in coumarin metabolism and highlights the importance of regulatory context in determining whether secondary metabolite accumulation improves or compromises plant stress resistance.</p>