Commercial muffins, often rich in saturated fat and simple carbohydrates while lacking sufficient dietary fibre and protein, do not adequately meet nutritional demands, especially in regions facing malnutrition. The development of muffins was optimised to enhance nutritional quality through protein complementation with underutilised regional ingredients: white beans and quinoa. Protein quality was assessed using the Digestible Indispensable Amino Acid Score (DIAAS) method with FAO reference standards. White bean, quinoa, and wheat flours had DIAAS values of 77, 50, and 34%, respectively. Muffins prepared with an optimal 25/50/25 blend of bean, wheat, and quinoa flours achieved a DIAAS of 72%. Key parameters, including protein, fat, dietary fibre, and phenolic content, were analysed using AOAC methods, alongside physical attributes such as texture, colour, and height. Sensory analysis and acceptance were evaluated using a 9-point hedonic scale. Results demonstrated that muffins with partial wheat flour replacement had significantly higher protein content (+ 15% and + 25%), dietary fibre (+ 30% and + 40%), and total phenolic content (+ 300% for both) compared to the control and commercial muffins, respectively (p <
0.05). Although the enhanced muffins exhibited reduced height and increased hardness, they were well accepted, scoring 6.4 on the hedonic scale with an acceptability index of 71%. These findings suggest that incorporating beans and quinoa into muffin formulations is a promising strategy for improving nutritional profiles while maintaining consumer appeal, which could help address nutrient deficiencies and chronic disease risks in vulnerable populations.