In this paper the effect of incorporation of Jackfruit seed flour and finger millet flour (8:16%, 10:14%, 12:12%, 14:10%, 16:8%) and baking temperature i.e., 170°C, 180°C and 190°C on the various physico-chemical quality characteristics and sensory score of cupcake was evaluated. The cupcake was prepared by replacing the refined wheat flour with the Jackfruit seed flour and finger millet flour. The various quality characteristics i.e., Moisture%, Protein%, Fat%, Fibre%, Ash%, Carbohydrates%, Browning index, Hardness (g), Gumminess, Chewiness, Cohesiveness, Adhesiveness, Springiness along with the sensory attributes i.e. color, flavor, texture and taste of the developed cupcake was evaluated. Response surface analysis was performed with the quality attributes indicated that cupcake prepared with Jackfruit seed flour 14% and finger millet flour 10% and baked at 170 oC results the best quality cupcake have best nutritional, textural and sensory qualities. The optimal product at quality consist of moisture content 23.830%, protein 4.723%, fat 11.820%, Fibre 2.233%, ash 1.566%, Carbohydrates 55.826%, Browning index 24.612%, Hardness 46.666g, gumminess 42g, Chewiness 24.666g, Cohesiveness 0.865g Adhesiveness 11.466g, Springiness 0.633g. The sensory score for the optimised sample were colour 7.9g, flavour 7.9g, taste 7.9g, and Texture 8.0g respectively.