Our study investigated the effects of the non-disulfide cross-linking enzyme transglutaminase (TG) on depolymerized dough when mixed with caffeic acid (CA) or endo-xylanase (XY). Both CA and XY significantly decreased the resistance to extension (Rmax) of the dough and increased its extensibility (E value). The reduced Rmax and increased E value with CA were restored by TG. However, TG had no effect on XY-added dough. Changes in paste viscosities were most apparent with the addition of XY. The decreased paste viscosity induced by XY was not restored by TG. TG with/without CA or XY did not improve the bread volume; XY alone significantly enhanced bread volume. Our results showed that a combination of TG and CA is effective to improve dough properties, but not TG and XY. Our study indicated that TG improves dough properties when phenolic acid is used to as a reducing agent of gluten’s disulfide cross-linkages. However, it has no effect when endo-xylanase is used to hydrolyze arabinoxylan’s glycoside linkages.