The present study was conducted to develop and assess nutritional and organoleptic characteristics of millet-based gluten-free muffins incorporated with ragi and soy flour blends. Three standardized recipe of gluten-free muffins T1– RF: SF: R (80:10:10), T2 –RF: SF: R (60:20:20), and T3 – RF: SF: R (40:30:30), were developed and their sensory, physicochemical, and microbiological characteristics were analyzed. The optimal ratio of ragi, rice, and soya flour blends (40:30:30) was found to be more acceptable than other developed muffins. The mean score of overall acceptability control muffins and muffins treatment were lies in the category to like slightly to like very much 6.18 to 8.14 respectively. The physical characteristics indicated height weight, and volume of muffins treatment were significantly (P≤0.05) increased than control muffins (T0) except density of muffins treatment. Incorporation of ragi and soy flour in the muffin’s recipe increases moisture, ash, and crude protein, while the treatment muffins had carbohydrate and crude fat content was significantly lower than control muffins. The proximate composition indicates that the moisture, ash, crude fiber, protein, crude fat, and carbohydrate content of the most acceptable muffins treatment T3 were 30.48 gm, 1.50 gm, 0.13 gm, 9.63gm, 0.23 gm and 58.03gm, respectively. The total bacterial count of control and most acceptable muffins treatment was 1.5×104 cfu/g, 1.2×104 cfu/g respectively. The results showed that the addition of 40 % of ragi and soya flour in the recipe has improved the sensory and physico-chemical characteristics of the treatment muffins, and consequently increased their nutritional value.