Certain medicinal plants utilized in the traditional ayurvedic system are poisonous when used raw, but are used following a detoxification process. The Ayurvedic Formulary of India (AFI) provides details about these detoxification (known as "sodhana") processes as per traditional procedures. This research endeavor aimed to uncover the fundamental principles underlying the detoxification approach applied to Plumbago zeylanica, commonly referred to as "swet chitrak", in which plumbagin is the primary toxic constituent. Both unprocessed and processed (detoxified) extracts as well as the detoxification media were subjected to analysis for secondary metabolites using different analytical techniques. This investigation revealed a reduction in plumbagin content, its conversion to epoxyplumbagin and zeylanone and a noteworthy decrease in cis- and trans-isoshinanolone during detoxification. Furthermore, it was confirmed that pure plumbagin when subjected to the same detoxification conditions, is partially converted into epoxyplumbagin, and that cis and trans-isoshinanolone showed interconversion. The current work establishes the chemical basis of the age-old traditional ayurvedic process of detoxification of P. zeylanica.