n this study, a developed wheat flour blend (F), consisting of a high content of non-starch polysaccharides, was fortified with cellulase (C) and a cellulase–xylanase complex (CX) and then processed via conventional and hybrid treatment methods. Dry heating (T), hydrothermal treatment (H) and extrusion processing (E) were applied without or with enzyme addition as hybrid treatments. Proximate composition and polysaccharide profiles selected techno-functional and structural properties of modified wheat flours, were analyzed. Conventional and hybrid treatments induced changes in polysaccharide fraction compositions (especially the arabinoxylans) and the rheology of modified flour. Dry heating caused an inconsiderable effect on flour composition but reduced its baking value, mainly by reducing the elasticity of the dough and worsening the strain hardening index, from 49.27% (F) to 44.83% (TF) and from 1.66 (F) to 1.48 (TF), respectively. The enzymes added improved the rheological properties and baking strength, enhancing the quality of gluten proteins. Hydrothermal enzyme-assisted treatment increased flour viscosity by 14–26% and improved the dough stability by 12–21%; however, the use of steam negatively affected the protein structure, weakening dough stretchiness and elasticity. Extrusion, especially enzyme-assisted, significantly increased the hydration properties by 55–67% but lowered dough stability, fat content and initial gelatinization temperature due to the changes in the starch, mostly induced by the hybrid enzymatic–extrusion treatment. The structure of extruded flours was different from that obtained for other treatments where the peak intensity at 20° was the highest, suggesting the presence of amorphous phases of amylose and lipids. The results can be helpful in the selection of processing conditions so as to obtain flour products with specific techno-functional properties.