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.