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Home - Cookies

Published: Mar 9, 2017 · Modified: Feb 24, 2026 by Amanda Powell · This post may contain affiliate links.

Healthy Chocolate Chip Cookies

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Chocolate chip cookies get a delicious makeover. These whole wheat chocolate chip cookies are made with almond flour, whole wheat flour and no refined sugar, but still tastes incredibly decadent. 

Irresistible healthy chocolate chip cookies without the guilt. No one will ever know these are better for you!

Why you'll love it

This recipe was born from a request from a long-time reader who wanted a whole wheat chocolate chip cookie recipe that had no refined sugar and some added nuttiness. i think this recipe more than delivers!

  • Wholesome ingredients - There are simple ingredients that pack a nutrients in every bite while still feeling like dessert. 
  • Amazing texture - Soft, a little chewy, with bits of dark chocolate chunks studded throughout. 
  • Great made ahead - This recipe develops more flavor over time if you let the dough chill. It also freezes raw or baked beautifully! 

Key ingredients & substitutions

These are unlike your typical chocolate chip cookies, so let's review the ingredients that make this cookie unique and any potential substitutions you might want to make. 

  • Whole wheat - I highly recommend using Bob's Red Mill or King Arthur Flour whole wheat as you will get the best final texture. White whole wheat flour also works really well here. 
  • Almond flour - A very fine ground almond flour works the best. It does add a little nuttiness to the cookies, but it complements the whole wheat flavor. Make sure they are from blanched almonds. You can process them in the food processor quickly if the brand you use is more coarse ground. 
  • Coconut oil - I like coconut oil in this recipe because it gives the cookies a soft texture i particularly enjoy, but if you want a texture that more closely resembles a classic soft and chewy cookie, you can use ghee or avocado oil. You can use solid or melted coconut oil.
  • Coconut sugar - To make these cookies refined sugar-free, we use coconut sugar, but you can use any sweetener you prefer. The sugar does give the cookies an initial coconut flavor when fresh from the oven, but it dissipates when the cookies cool.
  • Arrowroot - This adds to the soft and puffy texture of the cookies while giving it some chew. It is an alternative to cornstarch or omit entirely. 

How to make

The process of making this is exactly how you make regular chocolate chip cookies which makes it fairly simple! 

  1. Preheat your oven and line your cookie sheets with parchment paper. 
  2. Mix together the almond flour, whole wheat flour, baking soda, arrowroot starch, and salt together in a large bowl and set aside. 
  3. Beat together the coconut oil and coconut sugar together in the bowl of a stand mixer fitted with the paddle attachment until fully combined. Scrape the bottom and sides of the bowl. 
  4. Add in the egg and vanilla and beat until fully combined. Scrape the bottom and sides of the bowl again as needed. 
  5. Stir in the dry ingredients on low speed just until combined. Fold in the dark chocolate chips. 
  6. Portion the cookie dough into balls on your prepared baking sheets 1 ½ to 2 inches apart and flatten slightly. 
  7. Bake until golden brown. 
The best healthy chocolate chip cookies. Crisp on the outside with a chewy and buttery center - without the butter!

Amanda's expert tips

When dealing with ingredients like regular whole wheat flour, you want to be sure you aren't over measuring. It is important to fluff the flour and spoon it into your measuring cup and gently sweep off the excess on top, or you can use a kitchen scale to weigh. Do the same with the almond flour. 

The oils from the almond flour and coconut oil tends to keep the chocolate from sticking to the dough like a typical cookie dough, this is normal. Pressing them in and adding more to the tops once rolled works very well. 

If you want your cookie dough to spread more like regular cookies, you can lessen the amount of almond and whole wheat flour by about a tablespoon each or switch from coconut oil to ghee. Do not make both changes together. 

Storage notes

Keep your cookies in an airtight container for up to a week at room temperature. 

You can freeze baked or unbaked cookies. 

  • Freeze unbaked cookie dough by portioning them out and freezing them on prepared baking sheets for about an hour before transferring it to an airtight container. They can stay frozen up to a month.
  • Freeze baked cookie dough by leaving them in an airtight container with parchment paper between each layer of cookies. They can remain frozen for up to a month. 

When you are ready to bake or want to warm your frozen baked cookies, follow my guide on freezing cookie dough.

Recipe FAQ

Do I have to use almond flour?

No, if you would rather this be 100% whole wheat, you can substitute with 1 cup of flour instead of the almond flour.

Can I use something besides coconut sugar?

Yes, you can use any granule- type sugar you prefer. If you go for a sugar alternative like Stevia, I would use less sugar, about ¾ of the amount. 

I don't have coconut oil, can I use something else?

Yes, you can use a neutral oil like avocado oil. You can also use ghee or even melted unsalted butter. 

Refined sugar free healthy chocolate chip cookies. No one will ever even know these are better for you!

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Recipe Card

Irresistible healthy chocolate chip cookies without the guilt. No one will ever know these are better for you!

Healthy Chocolate Chip Cookies

Amanda Powell
Soft, chewy healthy chocolate chip cookies. All of the taste, but a lot more nutrient-rich
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 8 minutes mins
Total Time 23 minutes mins
Course Chocolate Chip Cookie Recipes
Cuisine American
Servings 24 cookies
Calories 125 kcal
Prevent your screen from going dark

Ingredients
  

  • 1 ¼ cups almond flour
  • 1 ¼ cups whole wheat flour
  • 1 teaspoon baking soda
  • 2 teaspoons arrowroot starch or cornstarch
  • ½ teaspoon salt
  • ½ cup coconut oil
  • 1 cup coconut sugar
  • 1 large egg beaten
  • 1 ½ teaspoons vanilla extract
  • 1 cup chocolate chips
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Instructions
 

  • Preheat the oven to 350 degrees F. Line two baking sheets with parchment paper.
  • In a medium bowl, mix together the almond flour, whole wheat flour, baking soda, arrowroot starch, and salt.
  • In a mixer, beat together the coconut oil and sugar until well combined. Add in the egg and vanilla extract then beat well.
  • Pour in the flour mixture and mix until just combined. Fold in the chocolate chips. The chocolate chips may look like they don't stick to the dough well, that is okay.
  • Make balls of cookie dough with about 1 ½ to 2 tablespoons of cookie dough. Roll into a ball and flatten slightly.
  • Place on the baking sheets about two inches apart.
  • Bake for 8 - 10 minutes, or until a light golden brown.
  • Allow to cool on a wire rack

Notes

  • Store in an airtight container for up to a week. You can also store in the freezer for up to a month.
  • For the best results, use your favorite dark chocolate chopped instead of regular chocolate chips.

Nutrition

Serving: 1gCalories: 125kcalCarbohydrates: 18gProtein: 3gFat: 10gSaturated Fat: 5gPolyunsaturated Fat: 4gCholesterol: 8mgSodium: 101mgFiber: 2gSugar: 12g
Keyword chocolate, chocolate chip, cookies, dessert
Tried this recipe?Tag me on Instagram! @acookienameddesire #acookienameddesire


 

 

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About Amanda Powell

Baker, photographer, and sometimes world traveler behind A Cookie Named Desire. Obsessed with helping people live life sweetly with delicious food to share with the special people in your life and creating lasting memories.

Reader Interactions

Comments

  1. Medha says

    March 11, 2017 at 11:13 am

    Love the combination of flours you used here- these look delicious and definitely don't compromise flavor for health 🙂

    Reply
5 from 2 votes (2 ratings without comment)

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Hey, I'm Amanda!

I am the baker and photographer behind A Cookie Named Desire. I'm a cookbook author, food science nerd, world traveler (sometimes) with a major weakness for cookies and cheese.

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