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The objective of this study was to decrease the phytic acid content and increase the soluble dietary fiber content of whole wheat bread. For this purpose, wheat bran was fermented with fresh bakers’ yeast and commercial endoxylanase enzyme prior to the laboratory-scale bread baking process. Fermented bran was used in the formulation of whole wheat bread production. The target values were to reach the 25% soluble fiber and to obtain 40% decrease in phytic acid content. After achieving the targeted reduction in phytic acid and increase in soluble fiber content in laboratory-scale baking trials, the method was used to design a new baking process for whole wheat and bran breads at large-scale. Two different fermentation procedures were applied. First, bran was fermented with fresh bakers’ yeast and then with commercial endoxylanase enzyme. In the second procedure, enzymatic treatment was carried out before yeast fermentation. After the fermentation processes, bran together with fresh bakers’ yeast was mixed to form developed dough and the dough was used in the industrial bread production process of the bakery. The decrease observed in phytic acid content of whole wheat bread was 85% and the increase in soluble fiber content was around 43%. The results indicated that, potential health problems can be minimized with the reduction of phytic acid content of whole wheat breads by the industrial method developed in the study. In addition, positive health effects of bran can be improved by producing whole wheat and bran bread with increased soluble fiber content.