Whole Wheat Chocolate Chip Cookies

When my city, Springfield, MO, was in self quarantine mode earlier this year, I found it very difficult to find all-purpose flour online or in stores (although admittedly I only tried one store because I was limiting the number of places I went).

As someone who bakes pretty often, this wasn’t a major deal—I had other flours I decided to experiment with and use that were already in my pantry. I had a good amount of whole wheat flour, so that was the inspiration for this whole wheat chocolate chip cookie recipe.

But you should know these whole wheat chocolate chip cookies are still, well, cookies. They are made with butter and sugar and a generous heaping of dark chocolate chips.

So if you are worried these will taste like “health food,” then fear not, because they simply taste like delicious homemade cookies. 🙂 I will say the whole wheat flour adds another level of texture as well as flavor—they almost taste slightly nutty to me.

Here’s a side-by-side comparison of all-purpose flour and whole wheat flour. Whole wheat is less processed—it contains all of the wheat kernel (ground up), whereas in all-purpose flour, part of the wheat kernel is removed.

I will put the full recipe in the printable recipe card below, but I did want to note that this whole wheat chocolate chip cookie recipe works best if you chill the dough in the refrigerator for at least an hour (up to overnight).

I did test it without chilling and although it’s still good (so if you can’t wait, I get it!), the cookies spread more and it was harder to get that soft center that I prefer in cookies.

If you find yourself with whole wheat flour, or are looking to get into whole wheat flour baking, this is a super simple and delicious recipe to start with. Happy baking, friends! xo. Emma

If you like these, check out my Chocolate Chip Cookie Bars or my Oversized Soft-Center Chocolate Chip Cookies!

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5 from 1 vote

Whole Wheat Chocolate Chip Cookies

Course Dessert
Cuisine American
Keyword chocolate chip cookies
Prep Time 1 hour
Cook Time 8 minutes
Servings 15 cookies
Author Emma Chapman


  • ½ cup butter softened
  • ¼ cup sugar granulated white
  • ¼ cup sugar brown
  • 1 egg
  • 1 teaspoon vanilla extract
  • ¾ cup flour whole wheat
  • ½ teaspoon baking powder
  • ¼ teaspoon salt
  • 1 cup chocolate chips dark or semi-sweet
  • flaky sea salt optional


  • In a medium mixing bowl, cream together the softened butter and sugars. Add the egg and vanilla extract and stir until just combined.
  • Add the flour, baking powder, and salt. Stir until a dough ball begins to form. Then stir in the chocoalte chips.
  • Cover and chill in the refrigerator for one hour, and up to overnight.
  • Spoon onto a baking sheet lined with a baking mat or parchment paper. Top with flaky sea salt, optional.
  • Bake at 325°F for 8-10 minutes, just until the edges begin to brown.
Credits // Author and Photography: Emma Chapman. Photos edited with A Color Story Desktop.
  • tried them yesterday , my first time making cookies ever , loved them , easy and yummy

  • 5 stars
    Made these last night and they were seriously so yummy! The kids loved them even though they are the slightly “healthy” version!!


  • In comparison, which flour would you say is better or healthier for you?

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