Kañihua (Chenopodium pallidicaule), a gluten-free Andean grain, has high biological and nutritional values, essential amino acids, essential fatty acids, vitamins and minerals; in addition, its seeds or grains have antimicrobial, antioxidant, antidiabetic and antihypertensive properties. Therefore, Ch. pallidicaule has great potential in the industry, but it is very little researched. On the other hand, Monascus ruber is an edible fungus widely used for the production of red pigments that have diverse biological activities with applications as food colorants and nutraceuticals that protect the body from degenerative diseases related to oxidative stress. In this novel study, Ch. pallidicaule flour was obtained from the solid-state fermentation of grains by Monascus ruber NRRL 1597. The Response Surface Method was used to optimize the fermentation process in relation to three factors such as glucose, sodium chloride and monosodium glutamate according to the Box–Behnken Design with 15 treatments. The dependent variables were L*, a* and b* belonging to the CIELAB color space. Modelling was performed with the R software. The results of the response variables were 40.99, 8.21 and 12.85 for L*, a* and b* with R² values of 0.85, 0.91 and 0.87, respectively. Therefore, pigmented flours were obtained with great potential for application in the food industry, which is increasingly demanding functional foods.