Whole Wheat Chocolate Chip Cookies

By Rachel Tiemeyer
January 6, 2022

A perfect Whole Wheat Chocolate Chip cookie does exist! These cookies are made with real food ingredients and came out soft and delicious. Husband and kid approved!

Whole wheat chocolate chip cookies on a plate

Why Make a Whole Wheat Chocolate Chip Cookie?

I know, I know. If you’re going to eat a cookie, just really go for it right? Most of the time I feel that way. I hold nothing back when it comes to Monster Cookies and Oreo Fluff. But, I don’t mind making a healthy substitution on a dessert every once in a while, especially when it doesn’t compromise the flavor.

This is the case for these cookies!

Whole wheat chocolate chip cookies

What Ingredients Do I Need for Whole Wheat Chocolate Chip Cookies?

Another great thing about this recipe is the simplicity. Check out the ingredients you will need.

  • White whole wheat flour (This wheat variety is very important. More on that below.)
  • Baking soda
  • Salt
  • Unsalted Butter
  • Brown sugar & white sugar
  • Eggs
  • Vanilla extract
  • Semisweet chocolate chips
A whole wheat chocolate chip cookie split in half

Use White Whole Wheat Flour!

If you spend much time browsing through our baked goods, you’ll find that we almost always use White Whole Wheat Flour (instead of Whole Wheat Flour). We’ve found that White Whole Wheat Flour yields much fluffier/lighter tasting results. It works in most recipes as a replacement for whole wheat flour. Here is a bit more about the difference between the two.

Other recipes that use White Whole Wheat Flour are:

Whole wheat white flour

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Cookie Dough Tips

  • The biggest difference I noticed in this Whole Wheat Chocolate Chip Cookie Recipe was that the dough was a bit drier. But after they were baked, I didn’t notice a difference in the texture.
  • Use a Silicone Baking Mats – They are a reusable non-stick option that I’ve grown to love.
  • Use a Small Ice Cream Scoop for scooping out the dough.
  • You can easily freeze the dough you don’t use. Here is a whole post on how to freeze cookie dough.
Whole wheat chocolate chip cookie dough scooped onto a silicone baking mat

Ready to give Whole Wheat Chocolate Chip Cookies a whirl?

Your kids will gobble them up and they’d be a great recipe to add on to a meal you are taking to others.

Whole wheat chocolate chip cookies, one with a bite taken out of it.


Whole Wheat Chocolate Chip Cookies

  • Author: Thriving Home
  • Prep Time: 20 minutes
  • Cook Time: 15 minutes
  • Total Time: 35 minutes
  • Yield: 2 dozen small cookies 1x
  • Category: Dessert
  • Method: Bake
  • Cuisine: American


These are the BEST EVER soft batch, whole wheat cookies. They include all real food ingredients but retain the flavor and texture of the classic version.


  • 2 cups plus 2 tablespoons white whole wheat flour (this wheat variety is very important!)
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 12 tablespoons (1 1/2 sticks) unsalted butter, melted and cooled until just warm
  • 1 cup packed brown sugar
  • 1/2 cup sugar
  • 1 large egg, plus 1 large egg yolk
  • 2 teaspoons vanilla extract
  • 11 1/2 cups semisweet chocolate chips


  1. Preheat to 325 degrees F. Line two large baking sheets with parchment paper or cooking spray.
  2. In a mixing bowl, whisk together the flour, baking soda, and salt.
  3. In a separate bowl, whisk together the butter and sugars until thoroughly blended. Beat in the eggs and vanilla until combined.
  4. Add dry ingredients into the wet ingredients and stir until combined. Stir in the chocolate chips.
  5. Scoop a heaping tablespoon per cookie and roll in a ball. Place dough balls on lined sheet pan, spacing them out so they won’t touch when baked.
  6. Bake until the cookies are light golden brown, the outer edges start to harden, and the middle is still soft and puffy, about 15 minutes or so. Note: If baking two sheet pans of cookies at a time, be sure to rotate top and bottom and turn them front to back halfway through the cooking time.
  7. Let cookies cool slightly on the pan and then transfer to a cooling rack using a metal spatula.

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