Bakery products are becoming an essential part of the human diet. Millets are the staple grains in Asia and African countries, and they are the super future food because of their nutritive and disease-preventive nature. Pearl millet is one of the most nutritious cereal grains, and its protein lacks gluten, which makes it a suitable base material for the preparation of gluten-free products. However, gluten is necessary because of its unique viscoelastic nature, which makes the most innovative bakery items. In this study, 50% refined wheat flour (RWF) has been replaced with pearl millet flour (PMF) to prepare a muffin, and a ghee residue is utilized to make a ghee residue powder (GRP) as a functional ingredient to replace whey protein concentrate (WPC) in the eggless muffin. Substitution of fat with GRP reduced the specific gravity of batter from 1.05 to 0.99; lightness value was considerably decreased, whereas the redness and yellowness values increased from 1.06 to 8.32 and 23.62 to 26.20, respectively. Replacement of RWF with PMF affected the lightness and specific gravity of the batter. Substitution with PMF and GRP reduced the viscosity from 13.83 Pa·s to7.08 Pa·s. Gelatinization temperature of batters varied with substitution of flour and fat with PMF and GRP. Muffin volume dramatically decreased from 56.19 to 36.84 cm3 with substitution of GRP and PMF. Weight loss was increased from 12.14 to 13.68% by substitution. The hardness and springiness were reduced with substitution. The GRP can replace fat up to 25%; thereafter, muffin’s quality characteristic reduces; hence, 50% PMF and 25% GRP combination give satisfiable muffin product.