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You’ll love this one-bowl easy recipe for the best whole wheat chocolate chip cookies ever! Packed with flavor and oh so good, these are hands down the softest whole grain chocolate chip cookies you’ve ever had. And no mixer is needed!

whole wheat chocolate chip cookies on a baking sheet with a small bowl of chocolate chips.
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I know everyone claims to make the best chocolate chip cookies. But truly, these really are the best whole wheat chocolate chip cookies around.

Even better, you’re just using one bowl! No mixer is needed for these delicious whole grain cookies.

If you’re looking for a chocolate cookie recipe that you can make in an air fryer, check out our Air Fryer Cookies. And if you’re out of brown sugar, check out our recipe for Chocolate Chip Cookies Without Brown Sugar.

Ingredients

a bowl of flour, sugar, chocolate chips, butter, an egg, and other ingredients on a marbled board.

For this recipe, you’ll need:

  • Whole wheat white pastry flour
  • Vital wheat gluten – substitution tips are in the printable recipe card.
  • Butter – I prefer salted, but if you use unsalted, bump up the salt by 1/4 tsp.
  • Egg – just one. Room temperature, please, and thank you.
  • White sugar
  • Brown sugar – brown sugar contains more moisture than traditional white sugar, which creates a super moist and delicious chocolate chip cookie.
  • Vanilla extract
  • Almond extract – optional but highly recommended.
  • Chocolate chips – the recipe card has a recommendation on how much to add, but chocolate really should be measured with your heart.
  • Salt – sea or table salt

What is Vital Wheat Gluten?

Vital wheat gluten is essentially highly concentrated gluten that has been extracted from wheat flour.

When baking with whole wheat flour, adding ~1 tbsp of vital wheat gluten per cup of whole wheat flour produces baked goods that have a good rise and a fluffier texture.

If you don’t have vital wheat gluten, you can add 1 tsp of baking powder to the cookie dough in this recipe.

Here’s How to Make Them:

*I’ll walk you through it here with some photos and tips, and you’ll also find a printable recipe card at the bottom of the post with exact measurements, etc. You can also click “jump to recipe” to skip down.

In a microwave-safe bowl, microwave the butter for 20 seconds. You want some of it melted, but the vast majority of the butter should be soft but solid.

Add the brown and white sugar and mix. Add the egg and vanilla and almond extracts and mix.

Two bowls showing cubed butter, and an egg in a bowl of batter.

Add the dry ingredients, and mix until everything is about 50% combined. Add the chocolate chips and mix. Optional: Refrigerate dough for an hour at this point.

Make balls about 2 inches wide and place them on a baking sheet lined with parchment paper. Bake for 10 minutes.

The cookies will still look slightly underbaked, but trust the process. This will give you the softest whole wheat chocolate chip cookie you’ve ever put into your food hole. Every oven is slightly different, so if the cookies still look raw in the middle, bake them for another 1-2 minutes.

Two photos - one photo of a bowl of batter with chocolate chips, and unbaked cookie dough on a baking sheet.

After removing the tray from the oven, let the cookies remain on the baking sheet for ~15 minutes before transferring them to cooling racks.

How to Store and Reheat

Storing Leftover Cookies: Allow the cookies to fully cool before storing them in an air-tight container at room temperature for 2-3 days.

Cookies need to be stored in an air-tight container to avoid getting stale. If the cookies get left out, check out my tips on how to soften cookies.

You can also roll the dough into balls and store them unbaked, in the fridge, for 4-5 days. I like to leave them at room temperature while the oven preheats. Bake as directed in the recipe card.

Reheating Leftover Cookies: Room-temperature cookies are a delight, but there is nothing like a warm whole wheat chocolate chip cookie!

To reheat leftover cookies, place 1-2 cookies on a microwave-safe plate and loosely cover with a damp paper towel. Microwave for 10 seconds at a time until the cookies are warmed though.

Freezing Cookies: You can freeze both cookie dough or baked cookies.

You can freeze the cookie dough balls on a parchment-lined baking sheet or plate for a few hours. Transfer them to a freezer bag and they’ll store for months.

You can bake them from frozen, but I prefer to leave them at room temperature for 30-60 minutes prior to baking.

Variations

You can easily personalize these cookies to make them your own.

Add in some chopped nuts (~1/2 cup), throw in some dried fruit, or mix and match the chocolate chips that you use.

I love using half semi-sweet and half milk chocolate. We’ve also tried this recipe with chocolate chunks, peanut butter chips, and/or butterscotch chips. But, let’s be clear, any kind of chocolate chips will be amazing, so do whatever your cookie-loving heart desires.

If you’re not used to cooking with whole wheat flour, you can always ease into the process by using half whole wheat pastry flour and half all-purpose flour.

You can also line an 8×8 baking pan with parchment, press the dough in, and make a cookie cake to cut into slices.

multiple cookies on parchment.

Frequently Asked Questions

Can I substitute whole wheat flour for all-purpose flour in chocolate chip cookies?

Absolutely! And because these cookies are whole wheat, you can feel good better about giving someone a sweet snack.

What happens if you use whole wheat flour in cookies?

Unlike their white flour brethren, whole wheat chocolate chip cookies have more fiber, and allow you to feel full on fewer cookies.

That being said, baking with whole wheat requires a slight bit of recipe adaptations to make sure you get results similar to all-purpose flour.

Does whole wheat flour make cookies taste different?

Yes, but in the best way possible!

Whole wheat flour provides a nutty and toasty flavor to these cookies. When I have run out of whole wheat flour and have to use all-purpose, I find the cookies are missing a depth of flavor.

What is the difference between whole wheat flour and all-purpose flour?

All-purpose flour has the wheat germ and bran removed and only the endosperm is ground. This produces a lighter (and brighter) flour than whole wheat. Most American all-purpose flour brands contain ~12% gluten content.

Whole wheat flour has been milled/ground with the whole wheat kernel. It’s hardier than all-purpose flour but is lower in gluten. Most American whole wheat flour blends contain ~9% gluten content.

Can I use all-purpose flour in this recipe?

No whole wheat flour? No problem. You can easily substitute all-purpose flour 1:1 for the whole wheat pastry flour in this recipe.

You’ll leave the vital wheat gluten out, but all other ingredients/measurements remain the same.

How Do I keep cookies from falling flat?

Cookies usually fall flat due to the temperature of the fat. In this case, we’re using delicious, delicious butter.

If your butter was too warm when the other ingredients were mixed in, when baked, the butter melts too quickly to allow the other ingredients to keep the cookie shape.

You can prevent cookie spread by making sure your butter isn’t too melty at the start. This recipe is written so that you don’t have to chill the dough if you don’t want to, but it never hurts if you’re not pressed for time.

Pro Tips/Recipe Notes

  • Both the butter and egg should be at room temperature for optimal results.
  • Make sure you spoon the flour into the cup, rather than scoop the measuring cup into the flour. This can pack the flour in, causing too much flour to be added, resulting in a dry cookie dough.
  • If you need allergy-friendly chocolate chips, we love the Enjoy Life brand.
  • To take these cookies to the next level, try making them with homemade brown sugar and homemade vanilla extract.

More Recipes Like This

A stack of cookies on a tray with parchment.
5 from 14 ratings

Whole Wheat Chocolate Chip Cookies

Prep: 10 minutes
Cook: 10 minutes
Total: 35 minutes
whole wheat chocolate chip cookies on a baking sheet with a small bowl of chocolate chips.
You'll love this one-bowl easy recipe for the best whole wheat chocolate chip cookies ever! Packed with flavor and oh so good, these are hands down the softest whole grain chocolate chip cookies you've ever had.

Ingredients 

Instructions 

  • Preheat oven to 350˚F degrees.
  • In a microwave-safe bowl, microwave the butter for 20 seconds. You want some of it melted, but the vast majority of the butter should be soft but solid.
    ½ cup salted butter (1 stick)
  • Add the brown and white sugar and mix. 
    ¼ cup white sugar, ½ cup brown sugar, packed
  • Add the egg, vanilla and almond extracts. Mix.
    1 egg, 1 tsp pure vanilla extract, 1/2 tsp almond extract
  • Add the dry ingredients, and mix until everything is about 50% combined.
    2 cups whole wheat pastry flour, 2 tbsp vital wheat gluten, 1 tsp baking soda, 1/2 tsp sea salt
  • Add the chocolate chips and mix.
    2 cups semisweet chocolate chips
  • Optional: Refrigerate dough for an hour at this point.
  • Make dough balls about 2 inches wide and place on a parchment-lined baking sheet. Bake at 350˚F for 10 minutes. They will look underbaked.
  • Allow the cookies to rest on the pan for ~15 minutes before transferring to a cooling rack.

Notes

  1. Both the butter and egg should be room temperature for optimal results.
  2. Vital wheat gluten is really a magic ingredient for these cookies. If you don’t have any on hand, you can sub in 1 tsp of baking powder, but the results will vary.
  3. Make sure you spoon the flour into the cup, rather than scoop the measuring cup into the flour. This can pack the flour in causing too much flour to be added, resulting in a dry cookie dough.

Nutrition

Serving: 1cookieCalories: 248kcalCarbohydrates: 29gProtein: 4gFat: 13gSaturated Fat: 7gCholesterol: 23mgSodium: 122mgPotassium: 173mgFiber: 3gSugar: 16gVitamin A: 180IUCalcium: 26mgIron: 1.9mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Dessert
Cuisine: American
Tried this recipe?Mention @sustainablecooks or tag #sustainablecooks!

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About Sarah

Helping you serve up budget-friendly sustainable recipes with a side of balanced living.
Come for the food. Stay for the snark.

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25 Comments

  1. I’ve been grinding our flour for years, thanks to you!  This is my only CC cookie recipe.  I love that its lower in sugar and makes a dense, chewy flavorful cookie.  5 stars

  2. This is now my go-to chocolate chip cookie recipe. I use sprouted whole wheat which gives them a heartier texture that I’ve grown to like. The first time I made these I started without reading the whole list of ingredients. By the time I saw “whole wheat pastry flour”, I was too far in to quit. So that mistake turned into my favorite cookies. In case anyone wants to know, yes you can sub out the pastry flour for sprouted. The cookies turn out denser but have an interesting texture. It all depends on how much you want to sacrifice for the sake of a chocolate chip cookie!5 stars