Among various size reduction techniques, high-energy ball milling is one of the most attractive means for plant-based foods. The objectives of the work were to investigate the influence of ball diameters (3, 6, and 13 mm) and milling time (2, 4, and 6 h) on particle size and microstructural properties of quinoa flours. Particle size analysis demonstrated that ball-milled particles were mostly in the range of nanoscales (122-295 nm). A longer milling time with larger balls significantly increased the particles to microscale (3.58 μm). The scanning electron microscopy displayed the conversion of quinoa starch granules into flakes after ball milling, however, the X-ray diffraction crystallinity peak observed at a 2θ value of 19 to 20° did not change. The AFM roughness parameters, arithmetic and squared mean heights of flours increased with increasing ball diameters. These results provided new insights for the application of ball milling, in particular in functional foods and pickering emulsion.