Healthy Chocolate Chip Cookies! Yes, it’s a thing, and no, they do not sacrifice on flavor or texture. These healthy chocolate chip cookies are incredibly chewy and perfectly sweet—no one will be the wiser! They’re made 100% with whole-wheat flour, are naturally sweetened, dairy-free and are lower in sugar than just about any other chocolate chip cookie recipe.

chocolate chip cookies arranged on parchment paper with a bowl of chocolate chips to the bottom left and salt to the top right

If you’re looking for healthy chocolate chip cookies with no refined sugar, you’re in the right place!

If you’re looking for dairy-free healthy chocolate chip cookies with coconut oil, you’re also in the right place!

If you’re looking for healthy chocolate chip cookies with almond or peanut butter, you’re in the right place. 

And if you’re simply looking for a healthier chocolate chip cookie recipe, well I’m glad you’re here! These cookies have been tested time and time again and I can confidently say, healthy factor aside, these are dang good chocolate chip cookies. But luckily for you and me, they also happen to be made with wholesome, clean ingredients. 

two cookies stacked on each other, the top cookie with a bite taken out and melted chocolate running down the middle

These cookies are:

  • Whole-grain
  • Dairy-free
  • Naturally sweetened
  • Chewy
  • Coconutty
  • Chocolatey 
  • Gooey when warm

What makes this cookie recipe “healthy”?

For starters, these cookies ditch the all-purpose flour for whole-wheat pastry flour, making them 100% whole-grain.

And instead of refined white and brown sugar these cookies rely on unrefined coconut sugar. Not only is it more natural, but it adds more flavor than brown sugar does!

In place of the butter, this recipe uses a flavorful combination of unrefined coconut oil and creamy natural almond butter. This combination makes these cookies dairy-free and lower in saturated fat than most cookies. Not to mention the heart healthy fat the almond butter adds!

close up of a chocolate chip cookie on a piece of parchment paper with chocolate chips and cookies scattered around

What you’ll need for this cookie recipe:

These cookies are packed with healthy and wholesome ingredients.

  • Whole wheat pastry flour (one of my favorite baking ingredients!)
  • Baking soda
  • Unrefined coconut oil – unrefined is more nutritionally dense than refined is. It’s also more flavorful! If you aren’t keen on coconut flavor, use refined coconut oil instead—it’s less flavorful.
  • Creamy natural almond butter
  • Coconut sugar
  • Eggs
  • Pure vanilla extract
  • Kosher salt & flaky sea salt
  • Bittersweet chocolate chips or chunks 
ingredients for cookies measured out in small bowls including eggs, flour, vanilla, coconut sugar, coconut oil, chocolate chips, salt

How to easy make healthy chocolate chip cookies

One of the reasons I love this recipe so much is that it doesn’t require a stand mixer, or even a hand mixer. All you need is a big bowl and a whisk.

Everything about this recipe is very straight forward, but the most important part is to pay attention to the mixing process and to do each round of mixing/resting (we’ll get there). And the chilling. The chilling of the dough—albeit annoying—is e.s.s.e.n.t.i.a.l. 

grid of step shots showing the process of making cookies: sugar, oil and eggs whisked together, addition of almond butter, sugar and almond butter mixed together, flour added to sugar mixture
  1. Whisk together the flour and the baking soda; set aside. 
  2. Whisk coconut sugar, melted coconut oil, egg, egg yolk, vanilla and salt together until smooth, about 30 seconds. Let the mixture rest for three minutes.
  3. Vigorously whisk the coconut sugar and oil mixture again for 30 seconds. Let rest for three minutes. 
  4. Vigorously whisk the coconut sugar and oil mixture again for 30 seconds. Let rest for three minutes. 
  5. Vigorously whisk the coconut sugar and oil mixture one last time for 30 seconds. Let rest for three minutes. (This process is important for dissolving the sugar and creating a chewy cookie.)
  6. Add almond butter to sugar mixture and vigorously whisk to combine for about one minute.
  7. Using a rubber spatula, add flour to sugar mixture (reserve about ½ teaspoon flour mixture to toss with the chocolate chips) and mix to combine. Have patience, it WILL combine. 
  8. Toss chocolate chips with reserved flour to coat; add to cookie dough and mix just to combine. 
  9. Using three tablespoons (#20 scoop) of dough at a time, roll dough into balls and arrange on a parchment-lined baking sheet. 
  10. Chill dough balls for at least 30 minutes.
  11. Arrange six dough balls on a parchment-lined baking sheet set two inches apart and bake 12–14 minutes (12 minutes will result in a gooey cookie, 14 will result in a chewy cookie). 
grid of step shots showing the process of making cookies: cookie dough in a bowl, chocolate chips in a bowl, chocolate chips added to dough
grid of step shots showing the process of making cookies: cookie dough balls, baked cookie, melted chocolate being pressed with a knife

Optional step: if you like the chocolate chips to look melty like mine do, use the handle of a piece of silverware to lightly swirl the chocolate immediately after the cookies have come out of the oven. However, this certainly isn’t necessary!

The second image in the above grid is what the cookies will look like if you do not swirl the chocolate.

Chill, chill, chill

It is SO important that you scoop and chill the dough soon after mixing up the dough. If you aren’t ready or don’t have time to form the dough into balls, pop the dough in the refrigerator to chill until you are.

Do not let the dough sit out at room temperature or the coconut oil could begin to separate from the dough. 

chocolate chip cookies arranged on parchment paper with a bowl of chocolate chips to the bottom left and salt to the top right

The importance of bake time

I give a range of baking times with this recipe for a few reasons. One, all ovens are different. Yours might run a little hot or it may run a little cool. Start checking them at 12 minutes, and when their edges feel set, pull them. 

The second reason I give a range is because this also depends on how you like your cookies. Less time in the oven results in a ooey gooey cookie. More time creates a chewier cookie—both variations are great it just depends on preference. Now, if you like your cookies more dough then cookie, then I would recommend pulling these out at 11 or even 10 minutes. 

How you measure flour matters

This is true for all baking, but especially whole-wheat baking—the way you measure flour really matters. Instead of dragging your measuring cup through the flour, you need to first fluff the flour. Yes, fluff. To do this, use a large spoon to stir the flour, do this a couple of times—this adds air to the flour and helps to unpack the compacted flour.

The second part is to not drag your measuring cup through the flour at all. Use that large spoon to spoon flour into the cup then level it off with a flat edge of a knife. 

Alternatively, you can also rely on a food scale. Which I find makes baking easier and more fun.

two cookies stacked on each other, the top cookie with a bite taken out and melted chocolate running down the middle

Baking with coconut sugar

Nowadays it’s pretty easy to find coconut sugar. If you’ve never bought it before, look for it in the baking aisle next to the other sugars.

I prefer coconut sugar over most refined sugars (regular cane and brown sugar) because it’s far less processed. But let me be clear, it’s still sugar and it’s still metabolized like sugar in your body. However, one of the benefits of coconut sugar is that it has a lower glycemic index than refined sugar, which means it’s metabolized slower in the body and causes a lower and slower rise in blood sugar levels.

Now that you have coconut sugar, you may be curious how else you can use it. You’re in the right place! Use coconut sugar in these Healthy-ish Cinnamon Rolls, Homemade Graham Crackers, and Healthier Puppy Chow.

chocolate chip cookies arranged on parchment paper with a bowl of chocolate chips to the bottom left and salt to the top right

Can you freeze the cookie dough?

Yes! This cookie dough freezes wonderfully! I recommend scooping and forming the dough into dough balls as directed in the recipe. Freeze the dough balls on a parchment lined baking sheet. Once frozen solid, transfer the dough balls to a resealable bag, or Stasher bag. Frozen cookie dough will last up to three months in the freezer.

When you’re ready to bake, arrange the frozen dough balls on a parchment-lined baking sheet as directed in the recipe. (No need to thaw the dough prior to baking—they’ll actually do better if you don’t.) From frozen, bake cookies at 375ºF for 14–16 minutes.

How long do these cookies last?

Store these healthy chocolate chip cookies at room temperature in an airtight container for up to 5 days—though they’re best eaten within 3 days.

Pro tip—pop one of these in the microwave for five to ten seconds and you will be in ooey gooey chocolate heaven!!

two cookies stacked on each other, the top cookie with a bite taken out and melted chocolate running down the middle

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two cookies stacked on each other, the top cookie with a bite taken out and melted chocolate running down the middle

Make sure to tag me @ZESTFULKITCHEN ON INSTAGRAM or tag #zestfulkitchen on social media if you make a recipe! 

Don’t forget, if you make these healthy chocolate chip cookies, leave a comment and rating below!

To pin this recipe and save it for later, you can click the button on any of the photos, or the red button on the bar below the recipe. Happy baking!

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chocolate chip cookies arranged on parchment paper with a bowl of chocolate chips to the bottom left and salt to the top right

Healthy Chocolate Chip Cookies

  • Author: Lauren Grant
  • Prep Time: 20 minutes + 30 minutes chill time
  • Cook Time: 30 minutes
  • Total Time: 1 ½ hours
  • Yield: 16 cookies 1x
  • Category: Dessert
  • Method: Baking
  • Cuisine: American

Description

The BEST Healthy Chocolate Chip Cookies! Super chewy and full of flavor, these cookies are 100% whole-wheat, naturally sweetened and dairy-free. Under bake these a bit for a super gooey cookie, or bake them as directed for the ultimate chewy chocolate chip cookie! 


Ingredients

Scale

Instructions

Whisk together flour and baking soda; set aside.

Combine coconut sugar, melted coconut oil, egg, egg yolk, salt and vanilla, whisk until mixture is smooth and no lumps remain, 30 seconds. Let mixture stand for 3 minutes then whisk vigorously for 30 seconds and rest for 3 minutes. Repeat process of whisking and resting 2 more times, ending with resting, until mixture is thick, fluffy, smooth and shiny. Whisk in almond butter and beat until thick, 1 minute.

Using a rubber spatula, stir in flour mixture (reserve ½ teaspoon flour to toss with chocolate chips) until nearly combined. Toss chocolate chips with reserved ½ teaspoon flour to coat; add chocolate chips to dough and mix just to combine.

Working with 3 tablespoons (#20 scoop) dough at a time, roll into balls and space 2 inches apart on prepared sheets.

Chill sheets with dough balls for at least 30 minutes.

Meanwhile, heat oven to 375ºF with rack set in middle position. 

Bake 1 sheet at a time until cookies are golden brown, puffy, and edges have begun to set but centers are still soft, 12–14 minutes, rotating sheet halfway through baking. Transfer sheet to a wire rack, sprinkle cookies with sea salt, and cool completely.

Store cookies in an airtight container at room temperature for up to 5 days (best within 3 days).


Notes

Unrefined coconut oil is more nutritionally dense than refined coconut oil. It’s also more flavorful, so if you aren’t keen on coconut flavor make these with refined as it won’t add as much flavor.

I recommend using salted and unsweetened natural creamy almond butter.

If these need to be strictly dairy-free, be sure to use vegan/dairy-free chocolate chips.


Nutrition

  • Serving Size: 1 cookie
  • Calories: 223
  • Sugar: 15g
  • Sodium: 177mg
  • Fat: 12g
  • Saturated Fat: 7g
  • Carbohydrates: 25g
  • Fiber: 1.5g
  • Protein: 4g
  • Cholesterol: 27mg

Keywords: healthy cookies, healthy chocolate chip cookies, chocolate chip cookies, healthy baking

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About The Author

Lauren Grant is a professional culinary food scientist, food writer, recipe developer, and food photographer. Lauren is a previous magazine editor and test kitchen developer and has had work published in major national publications including Diabetic Living Magazine, Midwest Living Magazine, Cuisine at Home Magazine, EatingWell.com, AmericasTestKitchen.com, and more.

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  1. I’ll be honest, I was a bit skeptical when I made the dough, but OH my gosh. These cookies are SO dang good. Super chewy, coconutty, and just the perfect amount of sweetness. the finish of salt is perfect too! Already making these again this weekend, thanks for the great recipe!