The, present study was carried out to maximizing the available and valuable sources of proteins of the agriculture plant`s waste and industry duties . So this research focusing on the nutritional and functional properties of defatted hibiscus, jojoba and pumpkin seeds flour. Analysis were carried out on defatted seeds, to determine proximate chemical composition , such as crude protein , ether extract, ash, crude fiber, amino acids and carbohydrate content.The latter was calculated by difference. Protein content ranged of 23.4, 28.0 and 53.5 % of dry mater base (DM) of jojoba seeds flour (JF),  hibiscus seeds flour (HF), and pumpkin seeds flours (PF) respectively. In addition, fat content ranged from 13.9 % to 33.8 % of HF and PF, respectively, while the highest fat content 54.9% obtained from JF. Antinutritional compounds, such as phytates detected in all flours, ranged from 0.23 to 0.5 g/100g DM. Functional properties of all flours were assessed, such as  water absorption index (WAI), water soluble index(WSI),  acid number (pH), foam capacity (FC) and foam stability (FS). All flours were excellent in their functional properties except FC and FS of PF was inferior good.  Amino acids compositions of these flours were also determined. The protein of these flour had abundant amount of total essential amino acids and higher than recommended by FAO/ WHO (1973). This research classified the amino acids of all seeds flour into groups to identify the flour potential for food supplementation in bakery and meat processed formulation. The nutritional value of the protein and its quality methods based on in vitro (chemical) and animal bioassays in vivo for assessment of protein quality have been developed by predicting protein quality depending on the determination of amino acids and calculated chemical scores, essential amino acid index (EAAI), amino acid / essential amino acids ( A/E ) ratio, amino acids score (AAS), estimated biological (BV) and calculated protein efficiency ratio ( PER ). An in vivo of protein quality depending on biological assessment using rats which depending on true digestibility percentage (TD), BV and net protein utilization (NPU) were investigated. By comparison, between their chemical estimation and bioassay, it's clearly view that, both of HF and PF had good quality protein; as expressed by their high TD, BV and NPU when compared to poorly JF. Both of these flours were significantly a quite similar to standard protein of casein. Meanwhile, jojoba flour had a considerable amount of antinutritional factors of simmondsin, which act as satiety inducers and impede bioavailability of protein. All of these nutritional values of the different flours HF and PF concluded those have an excellent protein and nourished sources. These flours could be potentially added to food system, such as bakery products, complementary foods and meat products, moreover JF have been promising not only their nutritive value but also for their responsibility to diminish satiety and reducing food intake for dietetic persons.