Value of the data •This data provided the untargeted metabolite profiling of compounds that can be expected from the leaves of D. stramonium. •This data provides information to researchers of herbal medicinal plants in designing effective drug discovery assays for the discovery of new therapeutic applications of compounds from D. stramonium. •This article provides a method for identification of compounds from medicinal plant extracts using untargeted LC-QTOF-MS/MS analysis.