Sesame (Sesamum indicum L.) and mustard (Brassica juncea L.) are largely cultivated oil seed crops in India. These seed meals are good source of protein as well as phenolic antioxidants. The seed residue (seed meal) after oil extraction are normally dumped and party utilized as cattle food supplement. This research in basically involve development of membrane based simple technique for isolation of the valuable antioxidants from seed meal and betterment of the quality of the seed protein. Ultrafiltration technique was used to prepare sesame protein isolate avoiding use of any chemicals and bioactive peptide fractions were prepared using enzyme membrane reactor. The functional properties of membrane processed protein isolates were found much improved compared to conventionally prepared protein isolate. The bioactive peptide fractions and isolated antioxidants exhibited equivalent antioxidant activity like commercial antioxidants. Adaptation and scaling up of the technique developed in this study can help the vegetable oil industries to earn more revenue from process waste materials.