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20 Whole Wheat Cookies (+ Healthy Recipes)

From chewy oatmeal to decadent fudge, these whole wheat cookies are sinfully scrumptious! 

With colder weather around the corner, I find myself craving baked goods more and more.

Occasionally, I opt for whole wheat in place of all-purpose flour.

Soft Chewy Chocolate Chip Cookies in a Baking Rack
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You know what they say, anything is healthy in moderation!

But with one simple switch, you’ll have more nutrients in your cookies.

No need to sacrifice flavor for nutrition, these cookies are delicious nonetheless!

Here are 20 of my favorite whole wheat cookie recipes.

1. Whole Wheat Chocolate Fudge Cookies

Is there any way to go wrong with a double chocolate cookie? No way!

If you’re craving a chewy, fudgy, and chocolatey cookie, look no further!

With a chocolate cookie and chocolate chips, these cookies are irresistibly decadent. 

Don’t skip out on the obligatory cup of milk!

2. Whole Wheat Chewy Chocolate Chip Cookies

Everyone has a favorite chocolate chip cookie recipe! This whole wheat version may be your new favorite after just one bite.

Whole wheat flour has a heartier texture than all-purpose flour.

But these are as buttery and soft as a traditional chocolate chip cookie!

The trick to chewy cookies is pulling them out as they start to turn golden brown.

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Otherwise, they end up crunchy rather than soft. 

3. Whole Wheat Peanut Butter Cookie

Peanut butter cookies are ridiculously easy to make, and a fan-favorite!

These whole wheat cookies have the sweet and salty flavors you love.

There are just six pantry staples required for these perfect peanut butter cookies.

Go ahead and make a double batch and share the cookies with those you love!

4.  Whole Wheat Oatmeal Cookies

We won’t get into the philosophical debate of raisins or chocolate chips.

But we can absolutely bake up a batch of tender and buttery oatmeal cookies in the meantime!

The hardest part of making oatmeal cookies is waiting for them to be done.

I love the combination of old-fashioned oats and whole wheat flour in this recipe!

Whether you like dried fruits or prefer candy bits, there’s no shame! 

5. Apple Cinnamon Oatmeal Cookies

With fall comes apple picking season! And everyone knows that apple and cinnamon are a match made in heaven.

You’ll love these cookies with a touch of sweet and tart apple in every bite!

The combination of oats, whole wheat flour, and apple bits is divine!

For some extra fall flavor, throw in some caramel bits before baking, too! Cinnamon caramel apples, anyone?

6. Whole Wheat Butter Cookies

Crumbly butter cookies are an essential sweet treat during the holiday season.

This recipe is perfect for gifting, entertaining, or simply enjoying.

Whether in fancy shapes or simple rounds, butter cookies always bring a smile to my face.

They’re perfect for coffee, and so easy to make!

In preparation for baking, be sure that all ingredients are at room temperature.

This will help the dough form bubbles for a crumbly cookie.

7. Whole Wheat Snickerdoodles

I’ve yet to find a snickerdoodle cookie that I can resist.

Whole wheat, low-carb, or gluten-free: all snickerdoodles are delicious to me!

There’s something about that perfect balance of sugar and spice.

The “and everything nice” comes with extra nutrients from the whole flour in this recipe.

This recipe yields fluffier snickerdoodles. Maybe not traditional, but absolutely delicious!

8. Whole Wheat Crinkle Cookies

Crinkle cookies are the perfect sweet treat for your vegan companions.

Oh, and the whole wheat flour adds protein, vitamins, and texture.

Bite into the crunchy exterior into the soft and fluffy chocolatey interior. These chewy cookies are the perfect holiday treat!

Serve them at a family gathering, or make them for those you love. Either way, the crowd will go wild for these crinkle cookies!

9. Healthier Gingerbread Cookies

For far too long, I found myself intimidated by gingerbread cookies.

Long gone are the days of intimidation with this healthy variation!

Warm-spiced gingerbread is made with molasses, spices, and other baking staples.

With whole wheat flour and coconut oil, these are a bit healthier, too!

They’re perfect for decorating, assembling gingerbread houses, or just snacking on. You can’t go wrong with gingerbread.

10. Whole Wheat Chewy Oatmeal Raisin Cookies

Some people love oatmeal raisin cookies. If you’re one of those people, this recipe is the perfect way to make your own!

Warm spices, wholesome oats and flour, and an obligatory heap of raisins are included.

I’m talking tender, fall-apart-in-your-hand, fall-flavored oatmeal cookies.

This recipe is perfect to freeze the dough and give frozen cookies to friends! Who can say no to warm cookies in a hurry?

11. Whole Wheat Pumpkin Cookies

If pumpkin can go in bread, coffee, and pie, why not cookies, too? Pumpkin cookies fit right in with the season!

With a more bread-like texture, you can imagine how moist and fluffy these cookies are.

This is from the pumpkin, sugar, and whole wheat flour in the recipe.

Sprinkle them with powdered sugar before serving, and enjoy!

12. Healthier M&M Cookies for Santa

If you’ve ever helped Santa scarf down cookies late at night, you know the guilt.

Don’t worry, Santa’s sweet tooth will still be satisfied with these cookies!

Start with a little butter and flour, fold in M&Ms, and gently combine with love. It’s so easy to make this recipe, kids will love helping out.

While this recipe features M&Ms, you could easily adjust for your preferences.

Candy bits of any kind are always welcome in my cookies!

13. Whole Wheat White Chocolate Cranberry Cookies with Sea Salt

Do yourself a favor and bookmark this recipe now! Cranberry and white chocolate are a match made in heaven.

In just 30 minutes, you’ll bite into a piece of heaven on earth.

I’m talking tender, buttery cookie with bits of fresh cranberry and white chocolate in every bite.

Using whole wheat pastry flour will result in softer textured cookies.

Regular whole wheat flour is denser than its finer pastry flour counterpart. 

14. Healthier Whole Grain Molasses Cookies

Bring on the childhood memories with some munch-worthy molasses cookies.

Though molasses is less popular than sugar, it’s always delicious!

This recipe talks you through preparing a stiff dough with a few ingredients.

Trust me when I say, these molasses cookies go as fast as you can pull them out of the oven! 

15. Whole Grain Double Chocolate Brownie Cookies

I’ll admit, I’m a sucker for a chewy, chocolatey brownie. Turn that into healthier cookies, and look out!

Seriously though, if you love brownies, you have to try this recipe!

With the texture of a cookie, these are easy to eat two or three at a time.

Though letting them cool is difficult, they’ll hold their shape better after cooling.

16. Monster Cookies

Don’t worry, there are no monsters in these cookies. They’re so darn delicious, that they’ll turn you into a cookie monster!

With peanut butter, M&Ms, and chocolate bits in every bite, you know they’re delicious!

With whole wheat flour and rolled oats, there’s a hint of health involved.

Imagine mashing up all your favorite cookies into one, thick and gooey cookie. That’s a monster cookie!

17. Healthy White Chocolate Red Velvet Cookies

Red velvet is one of those iconic flavors that fit any occasion.

From backyard barbecues to wedding dessert bars, these cookies don’t disappoint!

White whole wheat flour is used in these cookies for a finer grain texture in the cookies.

This with a light cocoa taste and white chocolate chips is perfection.

18. Brown Sugar Shortbread

As simple as they are, shortbread cookies are too good to pass up. 

This recipe takes just 30 minutes from start to finish! Oh, and it only has three ingredients to put together.

For a bit of extra flare, dip your cookies in melted chocolate before serving.

19. Gingersnap Cookies

Gingersnap cookies are a delicious meld of molasses cookies and gingerbread. They’re lacey, thin, and worth the effort!

You’ll notice that the ingredient list is longer than most cookies.

This is to achieve the perfect balance of ginger, spices, and slight sweetness. 

These cookies are the perfect holiday gathering cookie! Sugar, spice, and everything nice!

20. Whole Wheat Dark Chocolate Biscotti with Almonds

I’m finishing off this list with the most sophisticated cookie on this list. Biscotti is less cookie and more of a delicacy in my house.

This biscotti has the perfect crunch you want for a hot cup of coffee.

You can even dip them in melted chocolate for a touch of extra sweetness!

To make biscotti, you actually need to bake your cookie dough twice.

First, as a large log, then after slicing into fingerlike pieces.

20 Whole Wheat Cookies (+ Healthy Recipes)

Try these whole wheat cookies for healthy, tempting treats! From chocolate chip to peanut butter to oatmeal, these recipes are sure to please.


  • Whole Wheat Chocolate Fudge Cookies

  • Whole Wheat Chewy Chocolate Chip Cookies

  • Whole Wheat Peanut Butter Cookie

  • Whole Wheat Oatmeal Cookies

  • Apple Cinnamon Oatmeal Cookies

  • Whole Wheat Butter Cookies

  • Whole Wheat Snickerdoodles

  • Whole Wheat Crinkle Cookies

  • Healthier Gingerbread Cookies

  • Whole Wheat Chewy Oatmeal Raisin Cookies

  • Whole Wheat Pumpkin Cookies

  • Healthier M&M Cookies for Santa

  • Whole Wheat White Chocolate Cranberry Cookies with Sea Salt

  • Healthier Whole Grain Molasses Cookies

  • Whole Grain Double Chocolate Brownie Cookies

  • Monster Cookies

  • Healthy White Chocolate Red Velvet Cookies

  • Brown Sugar Shortbread

  • Gingersnap Cookies

  • Whole Wheat Dark Chocolate Biscotti with Almonds


  • Select your favorite recipe.
  • Organize all the required ingredients.
  • Prep a whole wheat cookie in 30 minutes or less!
Whole Wheat Cookies

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author avatar
Kim - InsanelyGood
Hey there! I'm Kim. I love running, cooking, and curling up with a good book! I share recipes for people who LOVE good food, but want to keep things simple :)

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