BACKGROUND The flours of two Andean crops, tarwi (Lupinus mutabilis) and kañiwa (Chenopodium pallidicaule Aellen), present an excellent nutritional profile for inclusion in vegan gluten‐free muffin formulations. In this study, the proximal composition and techno‐functional properties of tarwi and kañiwa flours, and the technological quality of batters and muffins (potato starch‐based) formulated with 50% of these flours were evaluated. RESULTS Andean flours have high protein, fiber, and fat content, and display high water and oil absorption. In premixes formulated with potato starch and Andean flours, a reduction in paste viscosity was observed due to starch dilution and lower water availability. Depending on their ability to interact with water, the batters formulated with these flours had a higher consistency. Confocal laser scanning micrographs showed that batters with Andean flours presented a complex matrix with dispersed starch granules surrounded by proteins and fiber fragments. Muffins made with Andean flours had a slightly lower specific volume than the control, but crumb hardness was not modified by tarwi flour (50%) and a mixture of tarwi (25%) and kañiwa (25%) flours. The intrinsic color of these flours modified crumb color, and their reducing sugar content also favored Maillard reactions in the crust. These color changes are desirable in gluten‐free products because such products are frequently pale due to their high starch content. CONCLUSIONS This study showed that tarwi and kañiwa flours are suitable for developing vegan, gluten‐free muffins of good technological quality and improved nutritional profile, adding value to these underutilized ancestral flours. © 2022 Society of Chemical Industry.