Quinoa is a nutrient-dense food that lowers chronic disease risk. This study evaluated the physicochemical and sensory qualities of fermented camel milk with 1, 2, 3, and 4% quinoa. The results showed that improvement in camel’s milk increased the total solids, protein, ash, fiber, phenolic content, and antioxidant activity more effectively. Fermented camel milk with 3% of quinoa flour exhibited the highest sensory characteristics compared to other treatments. Fermented camel milk enriched with 3% red quinoa flour was studied in obese rats. Forty male Wistar rats were separated into five groups: the first group served as a normal control, while groups 2–4 were fed a high-fat, high-cholesterol (HF)-diet and given 2 mL/day of fermented milk and quinoa aqueous extract. Blood glucose, malondialdehyde (MDA), low-density lipoprotein (LDL), cholesterol, triglyceride, aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), creatinine, and urea levels decreased dramatically in comparison to the positive control group, while high-density lipoprotein (HDL), albumin, and total protein concentrations increased significantly. Fortified fermented camel milk decreased the number of giant adipocytes while increasing the number of tiny adipocytes in the body. The results showed that the liver and renal functions of hypercholesterolemic rats were enhanced by consuming fermented milk and quinoa. These results demonstrated the ability of quinoa and camel milk to protect rats from oxidative stress and hyperlipidemia. Further studies are needed to clarify the mechanisms behind the metabolic effects of fermented camel milk and quinoa