Whole Wheat Cookies 

From chewy oatmeal to decadent fudge, these whole-wheat cookies are absolutely delightful! As the colder weather approaches, I can’t resist the temptation of freshly baked treats.

Sometimes, I choose whole wheat instead of all-purpose flour.

You know what they say – anything is healthy in moderation! And with a simple switch, you can add more nutrients to your cookies. Don’t worry, you won’t have to sacrifice flavor for nutrition; these cookies are still absolutely delicious!

Best Whole Wheat Cookies Recipes

Here are 5 of my all-time favorite whole-wheat cookie recipes.

Apple Cinnamon Oatmeal Cookies

With the arrival of fall, it’s apple-picking season! And we all know that apples and cinnamon go together like a dream.

These cookies are a real treat, with a delightful mix of sweet and tangy apples in each mouthful!

The blend of oats, whole wheat flour, and apple pieces is heavenly!

For an extra taste of autumn, why not add some caramel bits before baking? Who can resist cinnamon caramel apples?


  • Whole wheat flour – 1 cup
  • Rolled oats – ½ cup
  • Cinnamon – 2 tsp
  • Baking soda – 1 tsp
  • Salt – ¼ tsp
  • Unsalted butter (lightly melted) – ¼ cup
  • Brown sugar – ½ cup
  • Maple syrup – 2 tbsp
  • Egg – 1 large
  • Vanilla – 1 tsp
  • Finely chopped, peeled apple – ¾ cup
  • Lemon – ½


Let’s get started on making these delicious apple oatmeal cookies!

  • Preheat your oven to 350 degrees.
  • Now, in a mixing bowl, combine the flour, oats, cinnamon, baking soda, and a pinch of salt. In a separate bowl, mix together the softened butter, sugar, syrup, egg, and vanilla extract until it’s all well combined.
  • Next, let’s bring the wet and dry ingredients together. Mix them until you have a nice doughy consistency. Great! Now, take an apple, and cut it into small cubes, around 1/8″ to 1/4″ in size. Before adding the apple cubes to the dough, give them a little lemon juice bath to coat them evenly.
  • Alright, it’s time to add those juicy apple cubes to the dough. Mix it up nicely, then spoon the cookie dough onto a baking sheet. You can use a spoon or an ice cream scoop to do this.
  • Now, pop that baking sheet into the preheated oven and let the cookies bake for about 12-15 minutes. You’ll know they’re ready when they turn a lovely golden brown.
  • Once they’re done baking, take them out of the oven and let them cool for a bit. And there you have it! Enjoy your scrumptious apple oatmeal cookies, perfect for a sweet treat any time of the day!

Whole Wheat Oatmeal Cookies

Let’s not dive into the philosophical debate over raisins or chocolate chips, but we can definitely whip up some delightful and buttery oatmeal cookies in the meantime!

The most challenging part of making oatmeal cookies is the anticipation of waiting for them to be perfectly done.

I absolutely adore the blend of old-fashioned oats and whole wheat flour used in this recipe!

Whether you have a preference for dried fruits or candy bits, there’s no judgment here!


  • Butter, softened to room temperature – 1 cup
  • Packed brown sugar – 1 ¼ cups
  • Eggs – 2
  • Vanilla extract, store-bought or homemade – 2 tsp
  • White whole wheat flour – 1 ½ cups
  • Ground cinnamon – 1 ½ tsp
  • Baking soda – 1 tsp
  • Cornstarch – 1 tsp
  • Salt – ½ tsp
  • Old-fashioned oats – 3 cups
  • Optional adds-in * Chocolate chips (semisweet, butterscotch, etc.), chopped nuts (walnuts, pecans, etc.), dried fruit (raisins, cranberries, chopped apricots, etc.)


Alright, let’s get these delicious cookies going! Preheat your oven to 350°F. Grab a stand mixer and attach the paddle. Now, cream together the softened butter and sugar on medium-high speed until it turns light and fluffy, which should take about 3 minutes. Next, add in the egg and vanilla, and mix it up until everything is nicely combined, around 1 minute.

Now, in a separate bowl, let’s whisk together the flour, cinnamon, baking soda, cornstarch, and salt until it’s all nicely mixed. Gradually add this flour mixture to the buttery mix in the stand mixer while using medium-low speed to combine everything together. Don’t forget to add in the oats too, and keep mixing on medium-low speed until everything is nicely combined. If you’re feeling adventurous and want some extra goodies, you can add up to 2 cups of your favorite add-ins like chocolate chips or nuts. Just gently fold them in on low speed until they’re mixed in but don’t overdo it.

Time to shape the dough into lovely cookie balls! You can use a heaping small cookie scoop or simply a spoon, whatever works for you. Place the dough balls on a baking sheet covered with parchment paper. Now, pop them in the refrigerator and let them chill for at least 10-20 minutes.

Once they’re nicely chilled, it’s baking time! Bake those cookies for 10-12 minutes, or until you see the edges turning just set and slightly golden. Oh, the aroma will be amazing!

Now, don’t rush. Let those mouthwatering cookies cool down a bit on the baking sheet for about 5 minutes. Then, transfer them to a wire rack to finish cooling off.

Alright, they are ready to be devoured! You can enjoy them right away or keep them fresh in a sealed container for up to 1 week. If you’ve made a whole bunch and can’t finish them all in a week (which is hard to imagine because they’re so tasty), you can freeze the cookies for up to 3-4 months. Just take one out whenever you crave that delightful treat. Enjoy!

Whole Wheat Peanut Butter Cookies

Peanut butter cookies are incredibly easy to make, and they are a beloved favorite!

These whole wheat cookies offer the delightful combination of sweet and salty flavors you adore.

You’ll only need six basic pantry staples to whip up these perfect peanut butter cookies.

Feel free to double the batch and share these cookies with your loved ones!


  • Creamy peanut butter – ½ cup
  • Egg, beaten – 1
  • Honey – ¼ cup
  • Vanilla extract – 1 tsp
  • Baking soda – ¼ tsp
  • Whole wheat flour – 2/3 cup


Preheat the oven to 350 degrees. Line a baking sheet with parchment paper or spray with cooking spray.

In a bowl, mix together the peanut butter, egg, honey, and vanilla extract.

Add the baking soda and mix well. Fold into the flour.

Using a 1-inch ice cream scoop, carefully portion the dough into 12 bites. Roll the bites into smooth balls. Flatten the balls to ¼ inch thick. Use a fork to create the classic criss-cross pattern.

Bake the cookies for 7-9 minutes.

Allow them to cool, and then remove them from the baking sheet.


Everyone has their preferred chocolate chip cookie recipe, but this whole wheat adaptation might become your new favorite with just one taste.

Whole wheat flour has a more substantial texture compared to all-purpose flour.

However, these cookies are just as buttery and soft as traditional chocolate chip cookies! The key to achieving a chewy texture is to remove them from the oven as soon as they start to turn golden brown.

Otherwise, they will end up crunchy instead of soft.


  • Unsalted butter softened – ½ cup
  • Whole-wheat flour – 2 cups
  • Salt – ½ tsp
  • Baking soda – 1 tsp
  • Granulated sugar – ¾ cup
  • Brown sugar – ¾ cup
  • Egg – 1
  • Vanilla extract – 1 ½ tsp
  • Semisweet chocolate chips – 2 cups (12 ounces)


In a large bowl, combine the flour, salt, and baking soda. Set the mixture aside.

Place the softened butter in a mixer’s bowl and add the granulated sugar and brown sugar. Cream them together at medium speed. Add the egg and vanilla extract, and mix until well blended. Gradually add the flour mixture and mix thoroughly. Stir in the chocolate chips.

Chill the dough in the refrigerator for one hour or overnight.

Preheat the oven to 375F and prepare two baking sheets with parchment paper.

Scoop the chilled dough onto the baking sheets and position them on the center shelf of the oven. Bake for 8 to 10 minutes until the tops turn golden brown and the edges become firm (the centers will remain soft). Remove the cookies from the oven and allow them to cool completely.

Bake any remaining cookies and let them cool down completely before storing in an airtight container.

Whole Wheat Chocolate Fudge Cookies

Is there any way to go wrong with a double chocolate cookie? Absolutely not!

If you’re in the mood for a chewy, fudgy, and intensely chocolatey cookie, search no more!

Made with a rich chocolate cookie dough and filled with chocolate chips, these cookies are undeniably indulgent.

And of course, don’t forget to pair them with a comforting cup of milk!


  • Butter – 1 cup (2 sticks)
  • Granulated sugar – 1 cup
  • Dark brown sugar – ½ cup
  • Pure vanilla extract – 2 tsp
  • Eggs – 2 (large)
  • Unsweetened cocoa powder – ½ cup
  • Whole wheat flour – 2 cups
  • Baking soda – 1 tsp
  • Salt – ½ tsp
  • Semisweet chocolate chips 2 cups
  • Coarse salt, for topping, optional


Place one stick of butter on the kitchen counter to soften. Put the other stick of butter in a microwave-safe bowl and melt it completely in the microwave. Let the butter cool until it reaches a semisoft texture, either on the counter or in the refrigerator, for about 30 minutes.

In the bowl of a stand mixer fitted with the paddle attachment, combine the softened butter, microwaved butter, and both sugars. Mix until the mixture becomes fluffy. Add vanilla and eggs, and mix briefly until they are just incorporated.

In a separate bowl, whisk together cocoa powder, flour, baking soda, and salt. Add the flour mixture to the butter mixture and combine until there are no more dry flour particles visible. The dough should be sticky, but you should be able to touch it with your hands without it being too messy.

Stir in the chocolate chips.

Cover the top of the bowl tightly with plastic wrap and let the dough rest in the refrigerator for 30 minutes or up to 2 days.

When you’re ready to bake the cookies, preheat the oven to 350ºF. Roll the dough into balls slightly larger than a golf ball and place them two inches apart on a baking sheet lined with parchment paper or a Silpat. If desired, top each cookie with a pinch of coarse or flaky salt.

Bake the cookies for 8-9 minutes, depending on the dough’s temperature. The cookies should be puffy and soft. Allow them to cool on the baking sheet for 5-10 minutes before transferring them to a cooling rack to cool completely.

Tips For Making Whole Wheat Cookies

Here are some helpful tips to make your Whole Wheat Cookies absolutely scrumptious:

Choose the right flour: Opt for finely milled whole wheat flour as it adds a heartier taste and more nutrition compared to all-purpose flour. Look for high-quality brands like Prairie Gold for the best results.

Measure flour correctly: Since whole wheat flour is denser than white all-purpose flour, it’s important to measure it accurately. Use the “scoop and swoop” method when measuring flour to avoid overly dense cookies.

Don’t overmix the dough: When combining the flour mixture with the butter/sugar mix, avoid overmixing to prevent tough cookies. Stir until just combined.

Refrigerate the dough: After preparing the dough, refrigerate it for at least an hour or overnight until it becomes firm and cool. Chilled dough results in better-shaped and textured cookies.

Adjust baking time: For chewy cookies, bake them until they start turning golden brown, usually around 8 to 10 minutes. Overbaking can lead to crunchy cookies, so keep a close eye on them.

Get creative with mix-ins: Enhance the flavors and textures of your whole wheat cookies by experimenting with various mix-ins like chocolate chips, nuts, dried fruits, or caramel bits.

Proper storage: Keep your cookies fresh by storing them in a resealable container at room temperature. Enjoy them within 2 days for the best taste.

Freezing cookie dough: Want fresh cookies anytime? Freeze the cookie dough by scooping tablespoon-sized balls onto a baking sheet. Once firm, transfer them to a resealable bag and freeze for up to 2 months.


Is whole wheat flour good for cookies?

Yes, whole wheat flour is good for cookies. It offers a healthier alternative to traditional all-purpose flour, as it contains the bran, germ, and endosperm of the wheat kernel, providing additional fiber, vitamins, and minerals. Whole wheat cookies can be just as delicious as those made with all-purpose flour, and they offer the added benefit of nutty and wholesome flavors

Is whole wheat flour less calories?

Yes, whole wheat flour has fewer calories compared to all-purpose flour. In 1 cup of whole wheat flour, there are approximately 407 calories, while 1 cup of all-purpose flour contains about 455 calories

What is the best wheat for cookies?

The best wheat for cookies is whole wheat flour. It produces delicious cookies with a heartier texture and a deeper flavor compared to those made with all-purpose flour. Whole wheat flour adds nutrition and a nutty taste to cookies, making them a tasty and healthier treat.

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