Quinoa (Chenopodium quinoa Wild.) is a pseudo-grain that belongs to the amaranth family and has gained attention due to its nutritional properties and many health benefits to the human body. Therefore, this study was conducted to evaluate the effect of different proportions of cooked quinoa seeds on feed intake, body weight gain%, organ weights/body weight%, liver enzyme activity, lipid profile, kidney functions, serum glucose, leptin hormone, and antioxidant enzymes of rats suffering from obesity. Thirty male albino rats weighing (120 ± 100 grams) used in this study. Results showed that the proximate chemical composition of CQS contained 8.57, 14.61, 4.76, 3.34, 5.12, and 63.60 g/100g for moisture, total protein, fat, ash, crude fiber, and carbohydrate, respectively. The biological results indicated that feeding rats diets containing CQS resulted in significant improvements in percentage gain in body weight, organ weight, average feed intake, blood glucose, kidney functions, liver enzymes, blood fats, the hormone leptin, and the percentage of oxidative stress. In addition, microscopic examination of the liver and kidneys of rats in groups treated with different levels of CQS showed a noticeable improvement in the tissue structure of these organs. Wholesome bread was produced with proportions of 10, 15, and 20% of CQS. Sensory evaluation indicated that all wholesome bread samples had an acceptance greater than 75%. In conclusion, the current study indicates that CQS has improved biomarkers in obese rats, and we recommend using cooked quinoa seeds as an addition in the field of functional foods.