Bread samples were made with microorganisms universally present in traditional fermented foods in order to investigate the effect of microorganism enzymes isolated from these traditional fermented foods on the decomposition of allergenic proteins in wheat flour. The properties and functionality of the baked bread were then examined. An immunoblot assay using serum IgE of people with wheat flour allergy suggested that the allergenic proteins were albumin and globulin of the salt-soluble fractions. Bacillus subtilis JK (JK strain) isolated from traditional fermented food produced enzymes with high protease activity. The JK enzymes digested the globulin fraction in wheat flour. Bread was made by using the JK microorganism and yeast, and the specific volume was about 13% greater than bread containing yeast without the microorganism. The firmness, adhesiveness, and gumminess were all less. The mixed bread sample had a softer texture than the yeast bread, and the proportions of the total amount of free amino acids and branched chain amino acids were higher. The results of SDS- polyacrylamide gel electrophoresis and the immunoblot assay suggested that part of the allergenic salt-soluble proteins had been decomposed in the mixed bread.