Quinoa protein (QP) has emerged as a promising alternative to gluten-based proteins in food applications due to its nutritional value and gluten-free nature. This study aimed to investigate the effect of microwave (MW) combined lysine (Lys) on the dielectric and gel properties. With increasing Lys concentrations, the dielectric constant initially declined then rose, while dielectric loss showed an inverse pattern. MW processed samples exhibited deeper penetration than water bath (WB), with penetration depth initially dipping then rising with amino acid levels. The combo treatment enhanced electromagnetic wave absorption and optimized absorber thickness. Optimal gel thickness for MW heating was approximately 1 cm, ensuring uniform radiation penetration, high absorption, and efficient energy conversion. Infrared analysis showed reduced α-helix/β-sheet and increased β-turn/random coil structures. The red shift and fluorescence intensity indicated Lys-induced partial unfolding QP. Notably, 0.6 % Lys with MW maximized gel hardness, adhesiveness, chewiness, elasticity, and viscoelastic properties (G', G"), significantly improving texture and rheology. The results provided a promising approach for the development of high-quality and gluten-free quinoa-based products.