These chocolate chip cookies with whole wheat flour are a fresh twist on a classic! Chill the dough in the fridge for an hour before baking for soft, chewy cookies with rich, complex flavor.
My team and I spent months pursuing the perfect whole wheat chocolate chip cookie.
Our goal: Harness the complex, nutty flavor of whole wheat flour without overpowering the other ingredients or sacrificing a classic chewy texture. 20+ recipe tests, 10ish bags of flour, a dozen taste testers, and $150 worth of chocolate chips later (oof), I think we nailed it.
Use fresh, high quality whole wheat flour here (that dusty 3-year-old bag in the back of your pantry? This is not the time). Fresh wheat flour should smell nutty and slightly sweet - not sour or musty.
Finally, don't skip the 1-hour chill in this recipe: It lets the wheat flour absorb some moisture from the dough, which yields a softer cookie with more balanced flavor.
Ingredients
Find a full ingredients list with exact quantities in the recipe card below.
Before you start baking, we want to highlight a few quick things:
- Unsalted butter gives you more control over the final seasoning in baking. You'll need softened, room temperature butter for these cookies.
- Chocolate chips. This recipe works best with chocolate that leans bitter: Semi-sweet chocolate chips work well, although these bittersweet chocolate chips were actually our testers' favorite. You can also use chopped baking chocolate (à la our chocolate chunks cookies).
- All purpose flour helps control for some of the differences between whole wheat flour brands, ensuring your cookies turn out well regardless of what brand you use (see our note below).
Whole Wheat Flour
Use fresh whole wheat flour here: It should smell slightly sweet and nutty, but not musty or stale. (If the flour smells dusty, that's how the cookies will taste.)
Whole wheat flour encompasses a range of wheat varieties and processing methods, which means results can vary by brand. We tested a 100% whole wheat this recipe with a half-dozen flours; the cookies' thickness and spread were quite different from brand to brand. (Adding some all purpose flour to this recipe helps control for that variable, although we still recommend King Arthur Flours for best results when baking.)
Learn more about baking with whole wheat flour in our Everyday Artisan Bread course!
Use a kitchen scale
Measuring ingredients like flour by volume (with cups) is notoriously unreliable. Because each person fills a cup of flour a little bit differently, it's easy to accidentally use too much in a recipe and end up with dry, dense cookies.
But when you use a kitchen scale to measure by weight (in grams), you get a perfect measurement every time. So if you have a kitchen scale, please use it! (No kitchen scale? Measure ingredients like flour with the scoop and level method for best results!)
Step by step instructions
Mix the dough
Cream butter and sugars together in a large bowl until fluffy. Add eggs and pure vanilla extract; mix again until you have a light, fluffy mixture.
Equipment Tip: We used an electric hand mixer in these photos; you can also use a stand mixer fitted with the paddle attachment. We don't recommend mixing these cookies by hand (it's difficult to cream the butter and sugars manually).
Add the dry ingredients (flours, kosher salt, and baking soda); stir to combine. Add most of the chocolate chips (reserve a few for topping the cookies later!) then transfer dough to the fridge to chill for one hour.
Why chill the cookie dough?
Whole wheat flour contains the entire wheat kernel, which gives it a fair bit of texture. Chilling lets the whole grain flour absorb moisture from the dough, which softens any sharp wheat pieces and helps the flavors meld. The result is a softer, chewier cookie with more balanced flavor. Don't skip this step!
Bake
Line a large baking sheet with parchment paper or a silicone baking mat. Use a cookie scoop to portion out the chilled dough, leaving cookie dough balls about an inch apart on the cookie sheet. Press a few extra chocolate chips into the top of each dough ball (totally optional - this is just for aesthetics!)
Transfer to a preheated oven; bake until the edges are very lightly browned and the centers have puffed up. Let baked cookies cool for a few minutes right on the sheet pan, then transfer to a wire cooling rack to cool completely.
Pro Tip: Whole wheat cookies are a bit darker in color than cookies made with all purpose flour, so the browning around the edges won't be as noticeable here as it is with some other recipes (like our melted butter cookies or white chocolate pistachio cookies).
Storage
Store cooled cookies in an airtight container on the counter for up to 5 days, or freeze for up to 6 months. Defrost frozen cookies for a few hours on the counter when you're ready to eat them.
FAQs
Yes! Use the paddle attachment on low speed, and make sure to pause and scrape down the sides of the bowl a few times to ensure even mixing. Especially large mixers can sometimes trap pockets of flour at the bottom of the bowl of a stand mixer, so be sure to check that it is mixed thoroughly.
If you'd like to use all purpose flour, we recommend making our melted butter chocolate chip cookies, which were designed to use AP flour instead of whole wheat! If you swap all purpose flour for the whole wheat flour in this recipe, the texture may change quite a bit.
I will be honest: We tested this recipe with milk chocolate chips, and we kind of hated it. The milk chocolate just doesn't work as well with the earthiness of whole wheat flour - the cookies felt very one-note and not as much like a fun treat or dessert.
With so much whole wheat flour in this dough, you really need the contrast of a bright, bitter chocolate: We recommend using at least a semi-sweet chocolate chip variety, but encourage you to opt for a bittersweet or dark chocolate option if you can.
That said, if you prefer milk chocolate to dark chocolate, follow your own taste buds! Just know that it will make a pretty significant difference in the final flavor.
We tested a 100% whole wheat version of these cookies with several different brands of whole wheat flour, but each brand performed quite differently when it came to spread, texture, and height.
Our testers liked the 100% whole wheat versions of cookies made with King Arthur Whole Wheat Flour (both regular and organic), Wegmans store brand whole wheat flour, and Kroger store brand whole wheat flour. If you're using one of those brands, you can use 100% whole wheat here without affecting the final texture or shape of the cookies too much (although the whole wheat flavor will be stronger, so if you don't want a super in-your-face whole wheat flavor, we recommend just following this recipe as written).
If you're using another brand of whole wheat flour, we recommend making this recipe as written the first time, and increasing the amount of whole wheat flour slowly once you're comfortable with the dough.
We test all of our recipes with - and highly recommend - King Arthur Flours. They are high quality, have great flavor, and are remarkably consistent from bag to bag.
King Arthur Regular Whole Wheat flour or Organic Whole Wheat Flour will yield the best results in this recipe. Both are milled from hard red wheat and deliver rich, complex flavor without feeling dusty or stale.
We have also tested this recipe with store brand flours from Wegmans and Kroger with good results. We did test this recipe with Bob's Red Mill Whole Wheat flour, although that flour produced the densest cookies of the bunch.
We have not tested this recipe with locally milled whole wheat flours, King Arthur's Golden Wheat flour (which is milled from a hard white spring wheat, as opposed to a hard red wheat), or any whole wheat pastry flour. Whole wheat flours can vary quite a bit: If you use a different brand, it may require small adjustments!
Did you make this recipe? Leave a comment and star rating below to let us know how it turned out!
📖 Recipe
Whole Wheat Chocolate Chip Cookies
- Prep Time: 20 minutes
- Cook Time: 30 minutes
- Total Time: 50 minutes
- Yield: 20-24 cookies 1x
- Category: Cookies
- Cuisine: American
Description
Whole wheat flour brings a flavorful twist to these classic chocolate chip cookies!
Ingredients
- 113 grams unsalted butter, softened to room temperature (1 stick)
- 130 grams white granulated sugar (⅔ cup)
- 150 grams brown sugar (¾ packed cup)
- 6 grams vanilla extract (1 ½ teaspoons)
- 2 eggs
- 220 grams whole wheat flour (about 1 ¾ cups)
- 60 grams all purpose flour (about ½ cup)
- 4 grams kosher salt (1 teaspoon)
- 5 grams baking soda (1 teaspoon)
- 340 grams semi-sweet or bittersweet chocolate chips (about 2 cups)
Instructions
- Use an electric mixer to cream butter, white sugar, and brown sugar together for 3-5 minutes, until the mixture is fluffy. We used an electric hand mixer in the photos above; you can also use a stand mixer fitted with the paddle attachment.
- Add vanilla and eggs; mix again to combine.
- Add whole wheat flour, all purpose flour, kosher salt, and baking soda to the bowl; stir until just combined.
- Stir chocolate chips into the cookie dough (optional: reserve a handful of chocolate chips to top the cookies before baking). We recommend switching to a spatula here and mixing the chocolate chips in by hand for more even distribution!
- Chill cookie dough in the refrigerator for 1 hour. The wheat flour softens as it absorbs moisture from the dough, yielding a softer cookie with more developed flavor. Don’t skip this step!
- Heat oven to 375° Fahrenheit. Line a large baking sheet with parchment paper.
- Use a 3-Tablespoon cookie scoop to portion out the dough; place each dough ball 1 inch apart on your prepared baking sheet. Optional: Roll each cookie dough ball lightly between clean hands to smooth the edges, then gently press a few reserved chocolate chips into the top of each cookie. Note: This recipe makes quite a few cookies; you will likely need to work in batches.
- Bake cookies at 375° F for 11-13 minutes, until they are very lightly browned around the edges. Remove cookies from oven and let cool right on the baking sheet for 10-15 minutes, then move to a wire rack to finish cooling. Cookies may look a bit puffy right out of the oven, but the centers will sink down as they cool to form a beautiful, chewy texture.
- Serve immediately or store cooled cookies in an airtight container on the counter for up to 5 days
Notes
Please use a kitchen scale. Measuring by volume (with cups) is notoriously unreliable. For best results, use a kitchen scale and follow the gram measurements provided above. If you don't have a kitchen scale, measure flour with the scoop-and-level method for best results.
The brand of whole wheat flour matters a LOT here. We tested this recipe with several brands; each one behaved a bit differently. The all purpose flour in this recipe helps keep the dough as consistent as possible across whole wheat flour brands, although we always recommend King Arthur Flours for baking. This recipe works best with fresh, high quality wheat flour: It should smell nutty and slightly sweet straight out of the bag, but not musty.
Substitutions. Adjust the exact amount of chocolate chips to your liking. Swap some or all of the chocolate chips for additional chocolate (white chocolate chips, chopped baking chocolate), nuts (pecans, pistachios, walnuts, peanuts), or M&Ms. Add a pinch of flakey sea salt to these cookies just after baking if you like.
Nutrition
- Serving Size: 1 cookie
- Calories: 196
- Sugar: 19.7 g
- Sodium: 130.1 mg
- Fat: 8.5 g
- Carbohydrates: 29.2 g
- Protein: 3.1 g
- Cholesterol: 25.6 mg
More of our favorite chocolate chip cookie recipes
Liz
I'll just say the cookies are excellent and I had to hide them!! I used Einkorn w.w. flour..
Rhonda @ Life As A Strawberry
Glad you love them - hiding a few for later is totally okay with us!