Background and objectives: Kañiwa is a little-known Andean native grain with excellent nutritional value. It contains no gluten and, therefore, has potential as a raw material for gluten-free products. The aim of this study was to evaluate techno-functional, thermo-mechanical, and physicochemical properties of two kañiwa varieties (Cupi and Illpa Inia), in order to assess their potential as ingredients in gluten-free bakery products. Findings: The Illpa Inia variety presented superior thermo-mechanical properties, such as greater mechanical resistance and stability, as well as less protein weakening and starch retrogradation, which were related to the quantity of its proteins, fiber content, and strong associations between lipid and starch. Conclusion: Similarities in starch characteristics and differences in fiber, fat, and protein quality and quantity between kañiwa varieties were found. This resulted in higher resistance to withstand mechanical and thermal stress for the Illpa Inia variety. The small size of the starch granules in kañiwa contributed to further improvement in its resistance against mechanical and thermal stress. This variety of kañiwa represents a promising ingredient for the food industry. Significance and Novelty: The physicochemical, techno-functional, and thermo-mechanical characterization of flours of two Peruvian kañiwa varieties provided new information on the suitability of kañiwa for use in gluten-free baking. Kañiwa is an interesting and novel ingredient to be used in gluten-free products, enhancing the nutritional value of these products.