Lysine (Lys) and Arginine (Arg) (0.6%) was added to the quinoa flour to improve the textural quality and physical properties of gluten-free sponge cake treated with different heating methods. The gluten-free sponge cake fortified Lys and Arg increased cell density and surface area fraction, compared to water bath (WB) treatment, with the microwave (MW) treatment further enhancing these effects. Furthermore, MW combined Lys treatment showed the best texture characteristics of sponge cake. The water distribution determined by 1H NMR presented that water molecules are bound by the protein network structure. FTIR spectrum proved MW combined with Lys promoted the transition from disordered structure to ordered structure of protein in quinoa sponge cake, which enhanced the expansion of protein molecules and the exposure of hydrophobic regions, thus promoting protein aggregation. SDS-PAGE revealed when alkaline amino acids were present, they can regulate the ordered aggregation of protein molecules under MW alternating electric field, leading to enhanced intermolecular interactions. Finally, microstructure evaluations by SEM demonstrated MW combined with alkaline amino acids formed a stable three-dimensional gel network structure, thus improving the quality of gluten-free quinoa sponge cake. Therefore, the study findings pointed to the feasibility of using MW to improve the physical and textual quality of quinoa gluten-free food.