A new flour blend (F) composed of selected milling and leaving passages with a high content of non-starch polysaccharides underwent thermal (T), hydrothermal (H) or hybrid processing and was used along with cellulase (C) and cellulase-xylanase complex (CX) to produce bread. This modified flour can be considered a clean label product. In this study, blends of common and treated flours were tested for dough properties and rheology. The modified flours were added at 10 and 20% to the base wheat flour. A pan bread was then prepared to test their suitability for bread baking. Dough and bread properties were subsequently assessed. Accordingly, dough with added thermally, hydrothermally, and hybrid modified flours revealed differences in rheology. Addition of hybrid enzymatic-hydrothermal treated flour increased dough tenacity by 23% and baking strength by 26%, but decreased dough extensibility by 19%, whereas hybrid enzymatic-thermal modification increased water absorption by 6% and bread yield from 146.77% to 150.02% when modified flour was added at 20%. Breads with added modified flours demonstrated a 16% increase in bread volume, 8% lower baking loss, and 14% greater density, with no negative effect on color and texture. Thus, hybrid thermal-enzymatic treatment of the developed flours can be recommended as a suitable method for enhancing the utilization of waste flour fractions and increasing their value by enabling them to be considered as clean label bread improvers.