Fenhexamid is a widely used fungicide with one of the highest maximum tolerance limits approved for fruits and vegetables. The goal of this study was to examine if fenhexamid is metabolized by a nontarget organism, a Lactobacillus species (Lactobacillus casei Shirota), a probiotic strain of the human gastrointestinal tract. The assignment of bacterial derivatives of the xenobiotic fenhexamid was substantially facilitated by a metabolomic software based approach optimized for the extraction of molecular features of chlorine-containing compounds from liquid chromatography-electrospray ionization-quadrupole time-of-flight mass spectrometry data with an untargeted compound search algorithm. After validating the software with a set of seventeen chlorinated pesticides and manually verifying the result lists, eleven molecular features out of 4363 turned out to be bacterial derivatives of fenhexamid, revealing the O-glycosyl derivative as the most abundant one that arose from the fermentation medium of Lactobacillus casei Shirota in the presence of 100 μg/mL fenhexamid.