The growing demand of the cereal market, which demands quality products at low cost, has driven the development of new, more accessible wheat varieties. This study evaluated the technological quality of flours obtained from three new wheat varieties produced in Andahuaylas: Espigón de Oro (EOVF), the Gavilón (GVF), and the Andino (AVF) varieties, comparing them with a widely used plain flour (PF). Their proximate parameters, rheological, thermal, and structural properties, elemental composition, and functional groups were analyzed. The local flours (EOVF, GVF, and AVF) presented similar carbohydrate and fat contents, but higher ash, and lower moisture and protein content than plain flour. The rheology and thermal stability showed limitations associated with a less consistent dough and a more fragile structure, indicating lower gluten quality. Differential scanning calorimetry found gelatinization temperatures between 53.42 °C and 57.12 °C, with energy requirements (ΔH) of 1.08 to 1.23 J/g, while thermographic analysis revealed that component degradation began at 150 °C. Scanning electron microscopy micrographs revealed starch granules with varied shapes and a trimodal distribution. Elemental analysis showed a good energy contribution, with 47.9–54.6% carbon and 45.2–51.5% OH. The FT-IR spectra showed similar functional profiles among all the flours. These results suggest that flours from new wheat varieties have a low energy requirement for cooking, making them ideal for extrusion processes and for products with a soft and light texture. They also represent an excellent alternative to commercial flour for developing functional, infant, and easily digestible foods.