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Quinoa flour can be made from milled or unmilled grains. Unmilled grains produce a more coarse, nutritious flour, while unmilled grains are used to make a much smoother flour. In either case, the flour is typically a creamy yellow to ivory color. Quinoa is gluten-free, so quinoa flour can be safely used in gluten-free baking projects for people with gluten intolerance. Bakers should be careful, however, as quinoa flour may be processed in a facility which contains gluten, in which case it can become contaminated.

The remarkably high protein content of quinoa grains holds true in quinoa flour, with the protein content averaging around 17 %. Quinoa flour is also very high in dietary fiber. The high protein content can interfere with some baking, so many bakers recommend mixing quinoa flour with other flours, rather than using it alone.