Wheat flour is a common raw material in the food industry; however, Andean grains, such as quinoa and kiwicha, are gaining popularity due to their quality proteins, fiber, and bioactive compounds. A trend has been observed toward the enrichment of products with these Andean flours, with them even being used to develop gluten-free foods. However, evaluating interactions between raw materials during industrial processes can be complicated due to the diversity of inputs. This study focused on evaluating the technofunctional and rheological properties of wheat, quinoa and kiwicha flours using a simple lattice mixture design. Seven treatments were obtained, including pure flours and ternary mixtures. Analyses of particle size distribution, water absorption index, subjective water absorption capacity, soluble material index, swelling power, apparent density and physicochemical properties were performed. Additionally, color analysis, photomicrographs and Raman spectroscopy were carried out. The results indicate significant differences in properties such as particle size, water absorption and rheological properties between the flours and their mixtures. Variations in color and microstructure were observed, while Raman spectroscopy provided information on molecular composition. These findings contribute to the understanding of the behavior of Andean flours in baking and pastry making, facilitating their application in innovative food products.