White flour is highly processed and offers little nutrition. Substitute whole wheat flour in a one-to-one ratio or replace half of the recipe's flour with a high-quality whole wheat flour that will provide fiber, vitamins and minerals.

Since wheat flour can be denser, sift before using it. Increasing the wet ingredients in the recipe slightly will keep your cookies from being too dry. They may also need less time to bake, so keep an eye on them. If you don't like the consistency of whole wheat flour in your recipe, try whole wheat pastry flour.

White sugar is juice from sugar cane that has been highly processed with chemicals to remove all of the color and flavor. The high sucrose level can have a negative effect on the body's blood sugar. The easiest way to reduce the calories in your cookies is to simply use less sugar. You can usually remove up to one-third of the sugar in a recipe without any noticeable difference. Sugar does provide moistness, so increase the liquid in your recipe slightly if you reduce the sugar. You can also replace ¼ of the sugar with powdered milk.

You can also substitute white sugar with the less-processed raw sugar or sugar substitutes. One of the best alternative sugars is called succanat, which contains the whole sugar of the sugar cane and is dark brown. Succanat can be substituted for half or less of the sugar in the recipe. Experiment with replacing part of the white sugar with honey, real maple sugar, molasses or a natural sweetener called Stevia. Many recipes that use these sweeteners recommend adding a small amount of baking soda and less liquid ingredients.

Ingredients like shortening and butter make for a tasty cookie, but add a lot of fat and calories. You can replace the fat with pureed fruit. You can also use a healthy ingredient like coconut oil instead, but your cookies will turn out more cake-like than the original recipe.