In the current study, partially defatted coconut flour (PDCF) was prepared using deoiled cake obtained after virgin coconut oil processing. The proximate analysis of PDCF revealed the presence of 5.21% moisture, 14.03% fat, 21.34% protein, 46.39% fiber and 3.27% ash, along with prominent functional properties. Herein, muffins were prepared by incorporation of PDCF as a replacement of refined wheat flour (RWF) at 0, 25, 50, 75 and 100% flour blend. Significant changes in batter rheology were observed after 25 to 100% replacement of RWF with PDCF, which indicated a decrease in peak viscosity and final viscosity by 65.05 to 83.59% and 61.57 to 85.17% respectively, an increase in specific gravity of batter by 0.857–0.929 g/L. The prepared muffins had significant variations in colour of crust and crumb regions as represented by changes in L*a*b*, Hue angle (h°) and Chroma (C) and textural properties such as hardness, springiness, guminess, cohesiveness, chewiness, and resilience. Incorporation of 50% PDCF significantly (P < 0.05) increased the overall acceptability of the muffins (with a maximum score of 8.5), with a fiber content of 5.53 ± 0.23% and protein content of 7.57 ± 0.30%. Storage stability studies performed at 25 ± 2 °C for seven days revealed an increase in microbial count, and reduction in textural properties but both to be in acceptable regime.