Healthy cookies! These whole wheat chocolate chip cookies are made with 100% whole wheat flour. These chewy cookies taste delicious!

I try to add a little extra nutritional goodness wherever I can in our diet. These whole wheat chocolate chip cookies are made with 100% whole wheat flour for a bit of extra whole grains with dessert.
But are they good? Really, that’s the most important thing. There’s no point to eating a cookie if it doesn’t taste good.
And these cookies definitely taste good! The whole wheat gives them sort of a graham cracker taste, and the butter and brown sugar give them a rich caramel-y flavor.
How to make whole wheat chocolate chip cookies

Step 1: Begin by placing the butter and sugars in a mixing bowl. Unlike most recipes, this recipe begins with cold butter.

Step 2: Beat the butter and sugars together until combined.

Step 3: Next, mix in the eggs one at a time until combined.
Step 4: Add the vanilla, and stir in.

Step 5: Add the flour mixture, and stir to combine. Do not overmix. If you overmix, you’ll end up with tough cookies.

Step 6: Stir in the chopped baking chocolate.

Step 7: Scoop 1.5 tablespoons of dough and place on the prepared baking sheets.
Step 8: Bake.

Recipe Tips!
- Chocolate: I prefer either semisweet or bittersweet chocolate as the cookies are already fairly sweet. You could use chocolate chips or chunks in the cookies instead.
- Baking sheet prep: I like to use silicone baking mats, but parchment paper also works well.
- Don’t overbake! Do not overbake the cookies unless you want crispy cookies. The cookies should look soft and underdone in the middle and just golden brown at the edges.
Recipe FAQs
For this recipe, a finely milled whole wheat flour is best. I really like Prairie Gold’s whole wheat flour.
The cold butter helps to keep the dough from baking out. If you don’t use cold butter, you would need to chill the dough.

How to freeze
You can either freeze the unbaked cookie dough or freeze the baked cookies.
Freezing the dough
To freeze the dough, make the recipe through step 8. Scoop the cookie dough and place on a baking sheet lined with parchment paper or a silicone baking mat.
Don’t worry about spacing the cookie dough. You can place the scoops right up against each other.
Freeze the dough until frozen through. Remove the frozen scoops of cookie dough and place in a resealable freezer-safe container.
When baking, place the frozen scoops on the baking sheet. There’s no need to thaw the dough. Add about 3-4 minutes to the baking time.
Freezing the baked cookies
To freeze to the baked cookies, bake the cookies as-directed. Place the baked cookies on a wire cooling rack and let them cool to room temperature.
Place the cooked and cooled cookies in a freezer-safe container, and freeze for up to 1 month.

Storage
These cookies are best stored in an airtight container at room temperature. They are best eaten within 2 days.
More chocolate chip cookie recipes!
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Whole Wheat Chocolate Chip Cookies
Ingredients
- 2 ¾ cups whole-wheat flour measured correctly
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1 teaspoon kosher salt
- 1 cup cold butter cut into 1/2-inch pieces
- 1 ⅔ cups brown sugar packed
- ¼ cup granulated sugar
- 2 large eggs
- 1 tablespoon pure vanilla extract
- 8 ounces semisweet or bittersweet baking chocolate roughly chopped into 1/4- and 1/2-inch pieces
Instructions
- Preheat oven to 350F. Line two baking sheets with parchment or silicone baking mats. Set aside.
- In a medium bowl, whisk whole wheat flour, baking powder, baking soda, and salt together. Set aside. Check out the notes on measuring flour for tips.2 ¾ cups whole-wheat flour, 1 teaspoon baking powder, 1 teaspoon baking soda, 1 teaspoon kosher salt
- Add butter and the sugars to the bowl of a standing mixer fitted with a paddle attachment.1 cup cold butter, 1 ⅔ cups brown sugar, ¼ cup granulated sugar
- With the mixer on low speed, mix just until the butter and sugars are blended, about 2 minutes. Scrape down sides of the bowl.
- Add the eggs one at a time, and mix until just combined.2 large eggs
- Stir in vanilla just until incorporated.1 tablespoon pure vanilla extract
- Add the flour mixture, and stir in just until combined. Do not overmix.
- Add the chocolate, and stir in until just incorporated.8 ounces semisweet or bittersweet baking chocolate
- Scoop 1.5 tablespoon scoops of dough onto the baking sheet, leaving 2 inches between them.
- Bake the cookies for 10-15 minutes or until the cookies are golden brown at the edges and just set in the centers. The cookies should be slightly underbaked to stay soft and chewy. If you prefer a crispier cookie, bake an additional 1-2 minutes.
- Transfer the cookies still on the baking mat or parchment paper onto the counter to cool.
Notes
- Whole wheat flour: I use a finely ground 100% whole wheat flour in this recipe. More information about the type of flour is available above the recipe.
- Measuring flour: I highly recommend either weighing the flour or sifting/aerating the flour, lightly spooning, and then leveling the flour. Too much flour will cause the cookies to be dry or crumbly. For the weights, click on “metric” by the ingredients label above the ingredients.
- Salt: Or 1/2 teaspoon of table salt.
- Sugar: If you like cookies that aren’t as sweet, don’t pack the brown sugar.
- Chocolate: You can substitute chocolate chips or chunks if you prefer.
- Nutrition values are estimates.
Nutrition
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Comments & Reviews
Sarah says
I’m definitely a beginner baker. These came out great -first try! Will definitely make them again.
Kate Dean says
Thank you!