Guggulu (
Commiphora wightii
oleo-gum resin) is exported in more than 42 countries including developed countries like the United Kingdom and the United States of America. The demand for guggulu is more than its production. Various purification processes have been mentioned in Ayurvedic classical literature which are not explored well yet, so it is impossible to discriminate between purified and raw guggulu. In the present study, an effort was made where guggulu was purified by using cow urine and changes were analyzed by using high-performance thin-layer chromatography (HPTLC) and liquid chromatography–quadrupole time-of-flight–tandem mass spectrometry (LC–QTOF–MS/MS). In HPTLC analysis, three new bands (
R
F
0.31, 0.68, 0.74) and twelve other bands were observed including the bands of marker compounds guggulsterone E (
R
F
0.81) and Z (
R
F
0.85) at 254 nm. In LC–QTOF–MS/MS analysis, two new peaks at Rt 5.00 and 16.21 min were observed in cow urine-purified guggulu. After purification, all the peaks were resolute well which shows the effects of purification. Overall, in LC–MS/MS study, metabolites, viz
.,
5-(13′
Z
-nonadecenyl)resorcinol (Rt 8.31), 8
β
-hydroxy-3,20-dioxopregn-4,6-diene (Rt 10.33), guggulsterone E (Rt 12.99), guggulsterone Z (Rt 13.28), guggulsterol I (Rt = 15.19), mangiferolic acid (Rt = 15.27), 20(
S
),21-epoxy-3-oxocholest-4-ene (Rt = 15.75), and guggulsterol II (Rt 16.23) were identified. The present study reports the first time a comparative analysis of raw guggulu and cow urine-purified guggulu by using advanced analytical tools like HPTLC and LC–QTOF–MS/MS. This study may be helpful in the standardization of and quality control of raw guggulu and cow urine-purified guggulu used in various formulations of guggulu.