<p>Non-targeted metabolomics was employed to analyze metabolites in wet rice noodles fermented by <i>Burkholderia gladioli</i> pv. <i>cocovenenans</i> (BGC) to explore the potential formation of bongkrekic acid (BA). Three groups were incubated for 72 h: the pathogenic strain BGC 83756-inoculated group, the non-pathogenic strain <i>Burkholderia gladioli</i> (BG) 10574-inoculated group, and a blank control (BK) group. Metabolite dynamics were monitored using ultra-performance liquid chromatography-high resolution tandem mass spectrometry (UPLC-HRMS/MS). BA was not detected in either the BK group or the BG 10574-fermented group during incubation. In contrast, BA was first detected in the BGC 83756-inoculated group at 16 h of fermentation and reached a concentration of approximately 4,800 μg/kg in the late stages of culture. A total of 723 and 606 metabolites were identified in negative and positive ion modes, respectively. Differential metabolites, including BA, α-dimorphecolic acid, and calystegine B₅, were significantly upregulated in the BGC 83756-fermented group compared to the BG 10574-fermented group. Conversely, sinapic acid, saccharopine, 2-methylbutyrylglycine, and 2-keto-6-acetamidocaproate were significantly downregulated. The non-targeted metabolomics analysis of the BA biosynthetic pathway generally aligned with the <i>bon</i> gene cluster predictions, except for β-branching events.</p>