The application of alkaline extrusion in whole corn flour not only produces partial gelatinization of starch but also favors interactions between its components and releases natural hydrocolloids, modifying the rheological properties and suitability for application in gluten-free pastas or bakery products. The intensity of these modifications and therefore their rheological quality depend on the extrusion conditions. This work aimed to study the effect of alkaline extrusion temperature (70, 80 and 90 °C) at 40% feed humidity on the rheological properties of Cuzco corn flour and its dough. The increase in extrusion temperature had a significant effect (p < 0.05) on the degree of gelatinization of the flours (increase from 31.74 to 71.64%), which impacted their viscous properties. The degree of gelatinization, the formation of amylose–lipid–protein complexes and the soluble fiber content modified the rheological properties of the dough, decreasing the elastic modulus with increasing extrusion temperature. The most cohesive and elastic doughs were obtained at a lower temperature (70 °C), which presented greater resistance to kneading. This study will expand the use of whole Andean corn flour in gluten-free dough to obtain pastas and/or bakery products, reducing the use of food additivess.