This study was conducted in order to determine the effect of autoclave and microwave treatments on cookies. Wheat dough was treated in an autoclave (30 min), a microwave (1 min), and both autoclave and microwave (30 min/1 min). The treated dough was baked or non-baked and cookies quality was assessed. The pH, moisture content, color, and texture were measured, and sensory evaluation was performed. The pH showed a slight increase when dough was treated in a microwave (before baking) and decreased in both the autoclave and autoclave/microwave (after baking) treatments. The moisture content showed a significant increase, compared to the control, in autoclave treatments. Regarding surface color of cookies, lightness was decreased in all treatments and redness was higher compared with the control, except for microwave (before baking), and yellowness was lower compared to the control, except for microwave treatment (after baking). Hardness, gumminess, chewiness, and shear force showed a significant increase when dough was treated in an autoclave/microwave (after baking) compared to the control. In the sensory evaluation, color, taste, texture, shape, and overall preference of cookies treated with an autoclave/microwave (after baking) showed a low score. These results suggest that autoclaving and microwaving may reduce the quality of bread and that preparation of countermeasures is necessary.