Current work comprises of chemical investigation of flavonoids present in Pongamia pinnata (L) seed oil. Purification of flavonoids was established by using UV, FTIR, MS and NMR spectroscopic analysis. Three isolated flavonoids were identified as, namely, Kanjone, Pongapin and Lanceolatin-B. This work led to the development of easy isolation methods with improved yields and the future prospects of commercial scale processing of these flavonoids directly from plant source.