The increasing interest in improving the nutritional value of gluten-free products has prompted extensive exploration of various ingredients to create functional and valuable options in this field. This paper aims to study the suitability of using quinoa and papaya powder for improving the nutritive value of gluten free cookies. To achieve this quality of cookies were studied on the basis of proximate analysis, physical properties and sensory evaluation. Quinoa flour had the highest protein and fat content, with 15 g/100g and 3.59 g/100g, respectively. Papaya powder had significantly higher fiber and ash content (12.92 and 4.59 g/100g, respectively) compared to both rice flour and quinoa flour. It also contained a significantly higher amount of carotene (9.05 mg/100g). Substituting quinoa flour for rice flour led to noticeable increases in moisture, protein, fat, fiber, and ash contents. Similarly, papaya powder in gluten-free cookies resulted in increased moisture, fiber, and β-carotene content in the cookies. Furthermore, the addition of quinoa flour significantly increased the levels of all examined minerals. In terms of physical properties, the weight of the cookies increased with the incorporation of papaya powder and further increased with the addition of quinoa. The volume, diameter, and thickness remained relatively unchanged with the addition of papaya powder, while volume and thickness decreased significantly when quinoa was used as a substitute. Additionally, the specific volume decreased when both quinoa and papaya were included, which is consistent with previous studies. The acceptance test results indicated that the panelists preferred samples S3 and S4. Furthermore, the supplemented cookies, containing quinoa and papaya flours, had a relatively high essential amino acid balance, suggesting that they can improve amino acid intake for children with celiac disease. Addition of both quinoa and papaya powder as a replacer for rice flour in gluten free cookies improves its nutritional value without effecting its physical properties or consumer acceptance.