The absence of a gluten network remains the main technological limitation in developing high-quality gluten-free sponge cakes, leading to poor structure, reduced volume, and impaired texture. This study aims to develop a functional gluten-free sponge cake by partially substituting rice flour with amaranth flour (5 to 15%) and tiger nut flour (25 to 35%), while optimizing the formulation to achieve a 35–45% reduction in added sugar compared to the traditional control cake, in order to improve the antioxidant and technological quality of the product. Several formulations were compared to a positive control (wheat) and a negative control (rice) by combining physicochemical, biochemical, and crumb structure analysis. The parameters evaluated include weight loss, specific volume, moisture, water activity (aw), texture profile analysis (TPA), crumb cell analysis, color, antioxidant potential and sensory acceptability. This study showed that the incorporation of amaranth and tiger nut flours improved the functional, physicochemical, textural, antioxidant, and sensory properties of gluten-free sponge cakes. Among all formulations, F8, which consisted of 60% rice flour, 10% amaranth flour and 30% tiger nut flour with 60% sugar, exhibited the best overall performance (p < 0.05), with a higher specific volume (5.84 cm3/g), higher moisture content (28.76%) and lower water activity (0.58 for the crust and 0.54 for the crumb), the highest area fraction (27.73%), stronger antioxidant activity (1.80 mg AAE/g dw), and the highest sensory acceptability (7.23) (p < 0.05). These results highlight the potential of combining these flours to develop highly acceptable gluten-free bakery products.