ABSTRACTThe effect of flour type and dough rheology on cookie development during baking was investigated using seven different soft winter wheat cultivars. Electrophoresis was used to determine the hydrolyzing effects of a commercial protease enzyme on gluten protein and to evaluate the relationships between protein composition and baking characteristics. The SDS‐PAGE technique differentiated flour cultivars based on the glutenin subunits pattern. Electrophoresis result showed that the protease degraded the glutenin subunits of flour gluten. Extensional viscosities of cookie dough at all three crosshead speeds were able to discriminate flour cultivar and correlated strongly and negatively to baking performance (P < 0.0001). The cookie doughs exhibited extensional strain hardening behavior and those values significantly correlated to baking characteristics. Of all rheological measurements calculated, dough consistency index exhibited the strongest correlation coefficient with baking parameters. The degradation effects of the protease enzyme resulted in more pronounced improvements on baking characteristics compared with dough rheological properties. Stepwise multiple regression showed that the dough consistency index, the presence or absence of the fourth (44 kDa) subunit in LMW‐GS and the fifth subunit (71 kDa) subunit in HMW‐GS were predominant parameters in predicting cookie baking properties.