In this study, wheat flour characterized by a high content of nonstarch polysaccharides was fortified with enzymes and then subjected to low temperature (up to 85°C) extrusion cooking treatment. Conventional enzymatic hydrolysis with cellulase and cellulase–xylanase blend, as well as extrusion and hybrid enzymatic–extrusion treatments, was tested under variable conditions. Extrusion of wheat flour was applied at 23%–27% initial moisture at the temperature range of 40°C–80°C. Proximate composition, polysaccharide content, and its fractions, as well as rheological and technofunctional properties, were tested. Extruded and hybrid-modified wheat flour showed a significant decrease in fat, ash, insoluble fiber content, gelatinization beginning temperature, dough stability, starch gelatinization, amylase activity, starch retrogradation, and gluten performance index, whereas increased hydration capacity, max viscosity, setback, protein weakening, and solvent retention capacity were evidenced in the presence of all tested solvents. Soluble and insoluble fractions of nonstarch polysaccharides were, however, significantly different, especially if the hybrid cellulase–xylanase–extrusion method was applied to wheat flour. Moreover, the crystalline structure of wheat flour changed significantly after extrusion and hybrid treatments. In addition, the microstructure showed a significant agglomeration of the extruded flours due to starch gelatinization and formation of melted phase in all extruded and hybrid-treated flours, with visible fibrous particles coming from the outer layers of wheat grains as polysaccharide fractions. Extruded wheat flour, characterized by increased viscosity, hydration, and solvent retention ability, can be used as a “clean label” improver in mixtures for various bakery products, especially bread.