Quinoa is considered as a super grain due to its high nutrient content. The current study aimed to estimate the treated black quinoa flour by some treatments (sprouting, roasting and steaming) as well as the quality characteristic of gluten-free cupcakes with different substitution levels (25:100%) of treated black quinoa flour. Sprouting and steaming reduced the total phenolic compounds (TPC) (78.44 and 96.06 mg GAE/100g, respectively) whereas roasting significantly increased it (102.92 mg GAE/100g) compared to the raw quinoa (98.99 mg GAE/100g). Treated quinoa flour had significantly higher antioxidant activity (AA) compared with control, and the roasting treatment showed the highest AA value. All the treatments significantly reduced the anti-nutrients content (phytates, tannins and saponins) of treated quinoa flour while enhance the functional properties (WHC and OHC) compared to the raw quinoa flour. High nutritional and functional gluten-free cupcakes for celiac patients were prepared. The crude protein, fat, ash, and fiber contents significantly increased in the produced cupcakes as the quinoa substitution levels increased (25:100%). Developed quinoa cupcakes showed good characteristics due to their highest scores in numerous sensory characteristics. Concerning overall acceptability (OA) and acceptability index (AI), steamed cupcakes had the highest scores followed by roasted cupcakes. Although sprouted quinoa cupcakes had the least overall score among all processing methods, they still have a high acceptability index (more than 88%). Therefore, sprouted, roasted and steamed quinoa flour can be used as untraditional functional food ingredient for high nutritional value bakery products along with technological and health benefits.