Flour Differences

• Whole-wheat flour, both the traditional brown type and white whole-wheat flour, include the entire wheat germ, the part of the grain that sprouts, and the bran surrounding the germ. These flours have more fiber, fat and vitamins than all-purpose flour, which contains neither the germ nor the bran. Whole-wheat flour contains 14 percent protein and white whole-wheat flour contains 13 percent, while all-purpose flour contains only 11.7 percent.

Results of Substitution

• Because whole-wheat flours have more protein than all-purpose flour, they form a greater amount of gluten protein, which holds in gasses formed by leavening agents, like baking soda and baking powder. As a result, your cookies will not rise as they would if you substitute whole-wheat flours for 100 percent of the all-purpose flour. All-purpose flour also allows cookies to spread out more than they would if made with whole-wheat flours.

Recipe Differences

• Whole-wheat peanut butter cookies need more leavening agent than those made with all-purpose flour. One version with 1 1/4 cups of whole-wheat flour also calls for 3/4 teaspoon of baking soda and 1/2 teaspoon of baking powder. A recipe for the same amount of all-purpose flour uses 3/4 teaspoon of baking soda. Because baking powder and baking soda produce bubbles during different times during baking, using both agents ensures that your cookies will rise successfully.

Changing the Nutritional Values

• Substituting whole-wheat flour for one-half of the all-purpose flour in your peanut butter cookies increases the fiber in the cookies. You can reduce saturated fat by substituting vegetable oil for shortening on a 1:1 ratio and using 2 tablespoons of honey in place of 1/4 cup of the butter in the recipe. You can also use reduced-fat peanut butter instead of the regular version.