Effects of partial (50%) and total replacement of wheat flour with black rice flour on the phytochemical, physico-chemical, sensorial, and textural properties of muffins were studied. Partial or total replacement of wheat flour with black rice flour in muffins improved their nutritional and antioxidative properties with a positive effect on microbiological and color stability during the storage period in accelerated conditions. The low gluten muffins had an anthocyanin content of 27.54 ± 2.22 mg cyanidin-3-glucoside (C3G)/100 g dry weight (DW), whereas the gluten free muffins had 46.11 ± 3.91 mg C3G/100 g DW, with significant antioxidant values. Retention of 60% and 64% for anthocyanins and 72% and 80% for antioxidant activity after baking was found. The fracturability and hardness scores increased with the addition of black rice flour, whereas firmness and chewiness increased for gluten free muffins. The confocal analysis revealed a tendency of glucidic components to aggregate, with gathers of small bunches of black rice starch granules comprising anthocyanin. The results allowed designing two new value added bakery products, low and free gluten muffins, with significant high amounts of bioactive compounds, suggesting the functional potential of black rice flour.