Naringenin exposure altered auxin redistribution via VrPIN1 leading to morphological alterations and significantly reduced the protein precipitable tannins that further enhanced the protein accumulation and bioavailability. Flavonoid exposure is known to affect the antioxidant profile of legumes. However, a detailed study evaluating the effect of flavonoid naringenin on morphology and biochemical profile of legume is lacking. The present study is a novel report of improved in planta protein bioavailability and antioxidant potential of legume mungbean on naringenin exposure. The quantitative evaluation revealed significant protein accumulation (64-122μg/g FW) on naringenin exposure. Further, an increase in protein solubility and digestibility compared to control was evident. Naringenin mediated altered α-amylase activity improved the mungbean seed germination rate. Naringenin induced auxin redistribution and altered PIN formed transcript expression reduced lateral root density and increased stem length that was subsequently reverted on exogenous indole acetic acid application. Naringenin enhanced polyphenolic accumulation and improved the antioxidant potential of mungbean. Additionally, the responsiveness of the early gene of the flavonoid biosynthetic pathway, Chalcone isomerase to naringenin concentration was revealed indicating a probable feedback regulation. Further, the presence of alternate liquiritigenin biosynthesis was also evident. The present study, thus reveals the probable potential of phytochemical naringenin towards agricultural sustainability in the changing environmental conditions.