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Home » Irresistible cookies

Chocolate Fudge Whole Wheat Cookies

Published: Dec 20, 2019 · Modified: Feb 7, 2023 by Amy Sandidge · This post may contain affiliate links · Leave a Comment

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There’s nothing better around the holidays or any time of year, than a batch of gooey, fudgy, chocolate whole wheat cookies. I can guarantee these whole wheat chocolate fudge cookies will be your new favorite!

Whole wheat chocolate cookies stacked together.

Cookies are a perfect way to celebrate the holidays but they're also delicious year around!

If you love this homemade cookie recipe you might also enjoy these chocolate chip oat flour cookies and these chocolate chip cookies with rye flour.

Why You Will Love This Recipe

  • Chocolate fudge cookies are gooey and decadent.
  • Perfect to make for the holidays by decorating them with candy cane pieces and white chocolate for an extra delicious flair.
  • An excellent introduction to whole wheat baking. Many people are afraid to try baking with whole wheat pastry flour, but it’s not as complicated as it sounds and has many health benefits.
  • A tasty whole wheat cookie the whole family will love!

Ingredients

There's nothing too out of the ordinary needed to make a batch of these whole wheat chocolate chip cookies. You should be able to find them at your local grocery store. Here's what you need:

  • Flours: We will be using a combination of all-purpose and whole wheat pastry flours for making these whole wheat chocolate cookies.
  • Unsweetened Cocoa: I love to use Hershey's Special Dark Cocoa.
  • Leavening: This fudge cookie recipe uses both baking soda and baking powder.
  • Butter: Use real regular butter for added richness in your cookies.
  • Sugars: These whole wheat cookies are sweetened with both granulated and brown sugar. Using the brown sugar adds a bit more moisture and makes them softer.
  • Eggs: Gives the cookie their structure.
  • Milk: Just a bit to add more moisture to these cookies as whole wheat flour tends to absorb more liquid than regular flour.
  • Vanilla: For added sweetness and flavor. Be sure to use real vanilla extract and not imitation.
  • Chocolate Chips: Choose your favorite. I like to use a mix of semi-sweet and white chocolate but you can also opt for milk chocolate, dark chocolate chips, or even a mixture of any type of chocolate.
Whole wheat chocolate cookies stacked together.

How to Make Whole Wheat Chocolate Chip Cookies

Once you've gathered together all your ingredients, you're ready to get started mixing up the cookies.

  1. Start by preheating your oven and prepping your baking sheets with parchment paper.
  2. In a small bowl, combine your dry ingredients and set them aside.
  3. Add the sugars and butter to a mixing bowl and beat until nice and fluffy.
  4. Add the eggs, milk, and vanilla. Mix everything together until just combined. Be sure not to overmix.
Butter and brown sugar in a Bosch mixer.
Ingredients for chocolate cookies in a Bosch mixer.
  1. Add your dry ingredients to your wet ingredients. Mix again just enough to combine everything. It’s crucial that you don’t overmix at this stage.
  2. Add the chocolate chips and gently mix in until they are distributed evenly.
Dry ingredients added to the wet ingredients in a Bosch Mixer.
Chocolate chips added to whole wheat cookie dough batter.
  1. Use a scoop, and evenly distribute your cookies on a baking sheet. I usually get about 10 to 12 cookies per sheet. Leave space in between the cookies.
Woman scooping chocolate cookies onto a parchment-lined baking sheet.
  1. Cook your chocolate whole wheat cookies for about 10 minutes for a softer cookie or 13-15 for a crispier cookie.

How to Decorate Chocolate Fudge Cookies

If you are wanting to make these cookies a little more festive, how about adding a drizzle of white chocolate?

  1. Start by melting your white chocolate with a little coconut oil. I add coconut oil to make it easier to drizzle. If you don't have it, don't worry about it.
  2. Crush some candy canes in a bag. Then drizzle the cookies and while the chocolate is still soft, sprinkle with the crushed candy canes.
  3. Let the chocolate harden. Once the chocolate firms up these chocolate fudge cookies are ready to serve or package up.
Whole wheat chocolate cookies on the table before decorating.
Chocolate fudge Whole Wheat Cookies with white chocolate drizzle.
Chocolate cookies with whole wheat flour and drizzled with white chocolate and topped with crushed candy canes.

TOP TIP: If it isn't the holidays, you can enjoy these chocolate whole wheat cookies without any decoration or drizzle them with white chocolate. Skip the candy canes and add colored sprinkles to them festive for your special occasion.

How To Bake With Whole Wheat Flour

Working with whole wheat flour can seem intimidating, but it doesn’t have to be. There are some basic rules that I live by when I use whole wheat flour.

  1. I use whole wheat pastry flour. Whole wheat pastry flour has a lower amount of protein which keeps the cookies tender and soft.
  2. Be sure not to overmix the flour. This can make the cookies tough and nobody wants a hard cookie.
  3. Don’t overbake! The cookies will keep baking as you pull them out, so you want to pull them a little early to prevent them from overbaking. Like overmixing, overbaking may result in hard and dry cookies.

Expert Tips

  • My favorite unsweetened cocoa is Hershey’s Special Dark. You can use your favorite cocoa brand.
  • Use whatever type of chocolate chip you prefer. I like to use a mix of semi-sweet chocolate chips and white chocolate chips in these chocolate fudge cookies. This is one of the ways you can tailor-make these cookies for your family. If you prefer all one type of chocolate chip, then you can use them.
  • Skip the topping. If you don’t like white chocolate or don’t have the time for the extra step, you don’t have to do the topping. The cookies will still taste fabulous.

FAQ

How does whole wheat flour affect the cookies?

The whole wheat flour is nutritious and has a slightly nutty flavor. Make sure and use whole wheat pastry flour and use the tips above and no one will even notice these are healthier cookies.

Can you substitute white flour for wheat flour in this recipe?

Yes, you can. This recipe goes well both ways.

Does baking with wheat flour require more liquid?

Generally, yes. But in this recipe, adding more liquid won’t help the cookies. It’s far more important to make sure you don’t overbake your cookies. The more overbaked the cookie, the drier it becomes.

Whole wheat chocolate cookies stacked together.

More Whole Wheat Cookie Recipes

  • Einkorn Chocolate Chip Cookies
  • Oatmeal Raisin Pecan Cookies
  • Simple Carrot Cake Cookies
  • Tender Shortbread Stamped Lemon Cookies
Whole wheat chocolate cookies stacked together.

Chocolate Fudge Whole Wheat Cookies

Amy Sandidge
If you are looking for a jump into whole wheat baking, try this recipe. I like to use the blend of all-purpose flour and whole wheat flour. It has the added health benefits, while still mainting the
5 from 2 votes
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 10 minutes mins
Total Time 20 minutes mins
Course Dessert
Cuisine American
Servings 30

Ingredients
  

  • 1 ½ cups all purpose flour
  • ½ cup whole wheat pastry flour
  • ¾ cup unsweetened cocoa Hershey's special dark is my favorite
  • 2 teaspoon baking soda
  • ½ teaspoon baking powder
  • ½ teaspoon salt
  • 1 cup butter, softened
  • ¾ cup granulated sugar
  • ¾ cup brown sugar I love using dark brown sugar here.
  • 2 eggs
  • 2 tablespoons milk
  • 2 teaspoons vanilla
  • 2 cups chocolate chips I like to use a mix of semi sweet and white chocolate and everyone loved that as well.
  • 1-2 candy canes this is for the crushed candy canes on top, which are optional.

Instructions
 

  • Preheat oven to 350 degrees.
  • Line 3 baking sheets with parchment paper and set aside.
  • In small bowl, combine flours, cocoa, baking soda, baking powder and salt. Set aside.
  • In a stand mixer, or bowl ready with hand mixer (these can also be done by hand with a wooden spoon or spatula, you will just need good muscles to do it). Attach paddles to stand mixer if using. Place softened butter and sugars into mixing bowl. Beat on medium speed until they are light and fluffy. Scrape down sides of bowl as needed.
  • Add eggs, milk, and vanilla. Mix again, this time only to combine. After the eggs are added it is easy to overmix, so be mindful of this. Scrape bowl as needed.
  • Next add in flour mixture. Mix only to combine. Scrape down and mix again if needed.
  • Add chocolate chips and mix for just a few seconds.
  • Scrape down bowl and remove beaters.
  • Scoop cookies to baking sheet. Leave a few inches of spacing, these do spread a little. I placed about 10-12 per baking sheet, if that gives you a better idea.
  • With the size of cookie I made, check the scoop link in the post, my cookies took right about 10 minutes. Let me say too though, I like a very soft and tender cookie. If you like a crispier cookie, you will want to bake another 3-5 minutes.
  • Remove cookies from oven. Allow to cool for a few minutes on the pan, then with a spatula transfer cookies to a cooling rack. Continue to allow to cool.
  • If you are topping with the crushed candy canes, prep them now. I unwrap and place them in a plastic bag. The bag then goes on my wooden cutting board and is smashed with a rolling pin. It won't take much to break them up to the size you want for the cookies.
  • Next, place about ¼ cup white chocolate chips in microwaveable bowl. Place in microwave on HIGH for about 15 seconds. Continue to microwave for 10 second increments, until you can see little areas of melted chocolate. Once you see small areas, start mixing. Mix it for about 20 seconds before returning to microwave if needed. Once it is smooth, drizzle over cookies. Before the chocolate sets, sprinkle with the crushed candy canes. How much chocolate and candy canes you use is a personal preference. Some like a lot , some just a hint. We are generally a mid range family, as shown in photos.
  • Now, sit back and enjoy. You deserve it!

Notes

My favorite unsweetened cocoa is Hershey’s Special Dark. You can use your favorite cocoa brand.
Use whatever type of chocolate chip you prefer. I like to use a mix of semi-sweet chocolate chips and white chocolate chips in these chocolate fudge cookies. This is one of the ways you can tailor-make these cookies for your family. If you prefer all one type of chocolate chip, then you can use them.
Skip the topping. If you don’t like white chocolate or don’t have the time for the extra step, you don’t have to do the topping. The cookies will still taste fabulous.
Keyword chocolate fudge cookies, whole wheat chocolate chip cookies, whole wheat cookies
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Hi, I'm Amy! I am a culinary school graduate working to create a balanced approach to healthy recipes. My recipes are ones that the whole family can love.

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