These are the best whole wheat chocolate chips cookies, made with whole wheat flour in a 1:1 swap for all-purpose flour. Chewy and buttery, with plenty of chocolate and brown sugar, these are an enduring classic.
These are seriously the best whole wheat chocolate chips cookies! Inspired by the excellent whole wheat chocolate chip cookies from Kim Boyce's Good to the Grain cookbook, they're packed with that classic chocolate chip cookie taste we all know and love. And other than the whole wheat flour, these ARE the classic chocolate chip cookies we all know and love.
The rest of the ingredients are familiar pantry staples and the dough bakes up into perfectly chewy and flavorful cookies that can be made large or small. I love the hit of whole grain flour, and they're easily adapted to be gluten-free if you need it with oat flour (see my oat flour chocolate chip cookies recipe, or reduce the sugar a bit if needed, like in my low sugar chocolate chip cookies).
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Why You'll Love These Whole Grain Cookies
If you haven't read Good to the Grain, I highly recommend it! Boyce makes great use of all sorts of whole grain flours, from spelt to millet and more. In these whole wheat chocolate chip cookies, whole wheat flour adds a little natural sweetness and earthiness because of the bran and germ, which are not removed. I think it's such a lovely complement to dark chocolate and brown sugar!
- Perfect cookie taste: Lots of chocolate, lots of butter, and enough vanilla to tie it all together, these whole wheat flour chocolate chip cookies have it all.
- Easily adapted. You could use whole wheat pastry flour, spelt flour, or even all-purpose flour if that's what you have. And of course, gluten-free oat flour is a natural choice to make this recipe gluten-free.
- The more whole grains the better. It's now widely recognized that a dose of whole grains gives us more nutrients and fiber, things we all need! And why not tuck it into desserts for the best of both worlds?
Ingredients Needed
I've outlined below what you'll need to make these yummy cookies. The full ingredient amounts and detailed instructions are included in the recipe card lower down.
- Whole wheat flour - Whole wheat flour or whole wheat pastry flour (or white whole wheat flour) may be used interchangeably in this recipe.
- Rising agents - A combo of (fresh!) baking powder and baking soda helps the cookies to rise perfectly.
- Salt - I always use fine sea salt in my recipes. Table salt also works.
- Butter - I prefer unsalted butter so it doesn't compete with the sweetness of the cookie. Soften it to room temperature first—you should be able to gently press into a stick of butter with your finger—so it's easy to cream with the sugars.
- Brown sugar - Light or dark brown sugar is fine.
- Granulated sugar - For a bit more depth of sweetness, use all brown sugar.
- Eggs - Use large eggs at room temperature.
- Vanilla - Pure vanilla extract will give the best flavor, or try vanilla bean paste.
- Semisweet chocolate chips - Or finely chop your favorite bar of semisweet chocolate.
How to Make Whole Wheat Chocolate Chips Cookies
Here's a look at how to make these cookies. No surprises here!
- Combine dry ingredients: In a small bowl, whisk together the flour, baking powder, baking soda, and salt.
- Cream butter: In a large bowl using a hand or stand mixer, beat the butter and sugars until light and creamy.
- Add eggs: Beat in the eggs and vanilla.
- Combine: Mix the flour mixture in all at once.
- Add the chocolate: Stir in the chocolate chips. Let the batter rest in the fridge for at least 20 minutes then line baking sheets with parchment paper.
- Form the cookies: Use a tablespoon measure to scoop heaping tablespoons of the dough and roll them into balls.
- Bake: Place the cookies in the oven and bake at 350°F for about 16 minutes. Remove sheets from the oven, let the cookies cool for 5 minutes, then place cookies on a rack until completely cooled.
Baking Tip: Add Ins!
To dress up these cookies a bit, add nuts like chopped walnuts or go super decadent with mini M&M's or chopped candy bits. You can also swap in a different kind of chocolate chip, including milk chocolate or even white chocolate for a different flavor note. I also like 1 cup of shredded sweetened or unsweetened coconut!
More Cookie Tips
- Use room temperature ingredients. Bring the butter and eggs to room temperature for a bit before you add them to the dough. Or, heat the butter in the microwave for 10 seconds. In gluten-free baking, the butter and sugar must be properly aerated for the best results, so I try not to use butter that's too cool.
- Do a double batch of dough: To save some cookie dough for later, double the ingredient amounts and freeze half of the dough. Thaw the dough in the fridge then bake it according to the recipe directions.
- Bake as bars: To make these into chocolate chip cookie bars similar to my super deliciously buttery gluten-free chocolate chip bars, press the dough into a buttered and parchment-lined 9x13 pan and bake for 30-35 minutes.
- Make dairy-free: Use non-dairy butter in place of the of the butter.
- Make refined sugar-free: Substitute coconut sugar for the brown sugar and granulated sugar.
- Other flour - You can do an equal combo of whole wheat flour and all-purpose flour if you wish, or use spelt flour or whole wheat pastry flour instead of whole wheat flour.
- Make gluten-free - Make these cookies with gluten-free oat flour to make them gluten-free! Simply substitute 420 grams of oat flour for the whole wheat flour.
- Flaky salt - Top cookies with flaky sea salt for the perfect sweet-salty touch.
- Make ice cream sandwiches - These whole wheat chocolate cookies are PERFECT for making ice cream cookie sandwiches. Fill them with a big scoop of vanilla, chocolate, or caramel ice cream for a treat.
Storage Options
Here are some ways you can store both the cookies and dough if you want to prepare it ahead and use it another time:
Cookies
- Counter - Cookies will keep in an air-tight container at room temperature for 5 days.
- Fridge - Store the cookies in an airtight container in the fridge for up to 7 days.
- Freezer - Place cookies in an airtight, freezer-safe container or sealable bag in the freezer for up to 3 months. Thaw the cookies in the fridge before serving.
Dough
- Fridge - Store the cookie dough in an airtight container in the fridge for up to 5 days.
- Freezer - Place the cookie dough in a freezer-safe container or sealable, freezer-safe bag and store it in the freezer for up to 3 months. Defrost the dough in the fridge before baking it.
- As cookies - You can form the cookies, place them on a cookie sheet, place them in the freezer for about 20 minutes until hard, then transfer the formed cookies to an airtight freezer-safe container to make it easier on yourself when you're ready to bake them.
More Chocolate Chip Cookie Recipes
If you try this whole grain chocolate chip cookie recipe, please let me know! And if you have any questions, always feel free to reach out in the comments or by email. I hope you love it! ❤️
Whole Wheat Chocolate Chips Cookies
Chewy and perfect, these whole wheat chocolate chip cookies will become your new favorite.
Ingredients
- 1 cup unsalted butter
- 1 cup brown sugar, light or dark brown sugar
- 1 cup sugar
- 2 large eggs
- 2 teaspoons pure vanilla extract
- 3 cups whole wheat flour (420 grams)
- 1 ½ teaspoons baking powder
- 1 teaspoon baking soda
- 1 teaspoon fine sea salt
- 8 ounces chopped bittersweet chocolate or chocolate chips
Instructions
- Place two racks in the upper and lower thirds of the oven and preheat to 350°F. Line two baking sheets with parchment.
- In a large bowl, whisk together the flour, baking powder, baking soda and salt.
- In another large bowl, cream the butter and sugar with a handheld mixer or stand mixer just until the butter and sugars are blended, about 2 minutes. Use a spatula to scrape down the sides of the bowl. Add the eggs one at a time, mixing until each is combined. Mix in the vanilla.
- Add the flour mixture to the bowl and blend on low speed until the flour is barely combined, about 30 seconds. Scrape down the sides and bottom of the bowl.
- Add the chocolate all at once to the batter. Mix on low speed until the chocolate is evenly combined. Use a spatula to scrape down the sides and bottom of the bowl and if needed stir and knead the batter to incorporate all of the ingredients.
- Scoop mounds of dough about 1-2 tablespoons in size onto the baking sheets, leaving 3 inches between them.
- Bake the cookies for 16-18 minutes until set.
- Place the baking sheet on a rack for a few minutes, then transfer the cookies to the rack to cool fully. Repeat with the remaining dough. Cookies are best eaten warm from the oven or later that same day. They'll keep in an airtight container for up to 3 days.
Notes
- Use room temperature ingredients. Bring the butter and eggs to room temperature for a bit before you add them to the dough. Or, heat the butter in the microwave for 10 seconds. In gluten-free baking, the butter and sugar must be properly aerated for the best results, so I try not to use butter that's too cool.
- Do a double batch of dough: To save some cookie dough for later, double the ingredient amounts and freeze half of the dough. Thaw the dough in the fridge then bake it according to the recipe directions.
- Bake as bars: To make these into chocolate chip cookie bars similar to my super deliciously buttery gluten-free chocolate chip bars, press the dough into a buttered and parchment-lined 9x13 pan and bake for 30-35 minutes.
- Make dairy-free: Use non-dairy butter in place of the of the butter.
- Make refined sugar-free: Substitute coconut sugar for the brown sugar and granulated sugar.
- Other flour - You can do an equal combo of whole wheat flour and all-purpose flour if you wish, or use spelt flour or whole wheat pastry flour instead of whole wheat flour.
- Make gluten-free - Make these cookies with gluten-free oat flour to make them gluten-free! Simply substitute 420 grams of oat flour for the whole wheat flour.
- Flaky salt - Top cookies with flaky sea salt for the perfect sweet-salty touch.
- Make ice cream sandwiches - These whole wheat chocolate cookies are PERFECT for making ice cream cookie sandwiches. Fill them with a big scoop of vanilla, chocolate, or caramel ice cream for a treat.
Nutrition
Serving: 1 cookieCalories: 159kcalCarbohydrates: 28gProtein: 3gFat: 5gSaturated Fat: 3gPolyunsaturated Fat: 0.4gMonounsaturated Fat: 1gTrans Fat: 0.2gCholesterol: 26mgSodium: 178mgPotassium: 74mgFiber: 2gSugar: 17gVitamin A: 142IUCalcium: 31mgIron: 1mg
Disclaimer: Nutrition information is automatically calculated and is an estimate (I'm not a nutritionist and can't guarantee accuracy!). Even when not specified, be sure to check that all the ingredients you use are gluten free if you need them to be by reading labels on all packaging and/or confirming with the manufacturer.
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