The purpose of this study is to investigate the effects of starch extraction methods (alkali, wet-milling, and enzymatic) on the multi-scale structures and functional properties of quinoa starch. When the enzymatic method was compared with alkali and wet-milling, it showed higher protein content (2.39%), larger size of aggregated granules (44.1 μm), higher relative crystallinity (29.6%), scattering intensity (17.8 α.u.), absorbance ratio of 1047/1022 (0.9), single and double helical content (8.2% and 23.1%), FWHM ratio (2.1), and average molecular weight and radius of gyration (1.58 × 107 g/mol and 106.8 nm), respectively. Similarly, quinoa starch by enzymatic extraction had a higher onset (82.1 °C), peak (83.8 °C), and conclusion (86.3 °C) temperatures, as well as an enthalpy change (6.7 J/g). It further showed maximum hardness (238.8 N), gumminess (105.6 N), chewiness (80.2 N), SDS content (7.5% of raw and 4.8% of cooked), and RS content (15.5% of raw and 13.9% of cooked), whereas it contained minimum RDS content (77.1% of raw and 81.9% of cooked). The results suggest that extraction of starch by the enzymatic method could be a viable approach to retain the native structure of starch and may eventually improve the glycemic response.