Demanding needs for quinoa flour increase rapidly in China in the last years. However, the investigations on quinoa flour are limited. In this study, defatting and extruding treatments were applied to develop novel quinoa flours with improved physicochemical and storage properties. Defatting treatment did not significantly affect the hydration, microstructure, pasting, and rheological properties. However, it revealed an effective means of lipid oxidation prevention. On the other hand, the extruding treatment showed slight affections on proximate composition. The decreased lightness, and increased yellowness, water adsorption index, water solubility index, and swelling power were observed. Furthermore, attributed to the completely starch gelatinization, a smoother surface microstructure, the lowest pasting temperature, the disappeared endothermic process, the decreased viscosity, and the highest tan delta value was obtained for the extruded flour, indicating that this flour had advantages in food formulates for certain food applications, like food for elderly or weaning food. However, extruded quinoa flour showed poor storage behavior for the highest peroxide value and malondialdehyde value. The findings above were hoped to provide a scientific basis for industrial quinoa flour development in the future.