Healthy Chocolate Chip Cookies

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These healthy chocolate chip cookies are soft, chewy and guaranteed to satisfy any sweet tooth. They’re made with whole wheat flour, coconut oil, Greek yogurt and coconut sugar. There’s no butter and no chilling required!

Healthy eating 100% includes treats in my book! While I don’t go crazy with cookies, I try to make upgraded recipes with small changes to make them a bit healthier. This chocolate chip cookie recipe is a perfect example. I made a few small swaps and the end result is a delicious cookie that no one will know is a healthy cookie!

Three healthy chocolate chip cookies stacked on top of each other. The top cookie has been cut in half, exposing the inside.

Why You’ll Love This Recipe

  • Everyone needs a classic chocolate chip cookie recipe in their back pocket!
  • These cookies are made with healthy ingredients but no one will be able to tell the difference between these and a traditional recipe.
  • They come together in no time at all and no chilling of the dough is required!
Ingredients measured out to make healthy chocolate chip cookies: egg, dark chocolate chips, sea salt, whole wheat pastry flour, baking soda, vanilla, Greek yogurt, coconut sugar and coconut oil.

Ingredients Needed

  • whole wheat pastry flour – whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy bread that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour. If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • baking soda – helps the cookies rise.
  • sea salt – brings the flavors together and also helps the cookies rise a bit!
  • coconut oil – instead of butter, we’re using coconut oil. You want the oil to be in a liquid state so warm a bit if necessary.
  • Greek yogurt – replaces some of the oil in this recipe. I recommend allowing the yogurt to come to room temperature prior to mixing. I haven’t tested it with vegan Greek yogurt but I’m sure that would work!
  • coconut sugar – to keep things refined sugar-free we’re using coconut sugar instead of white sugar. White sugar also works in a pinch!
  • vanilla extract – a flavor enhancer.
  • egg – helps structure the cookies by holding the fat and liquid components together. Let this come to room temperature before mixing into the dough. I haven’t tested this recipe with a flax egg, but I bet it would work. Let me know if you try it in the comments below!
  • dark chocolate chips – I really like Lily’s chocolate chips because they’re dairy-free and lower in sugar.
Collage of 6 photos showing the steps to make healthy chocolate chip cookies: mixing dry ingredients, mixing wet ingredients, adding the wet to dry, stirring in chocolate chips, flattening cookie dough balls with a spoon on a cookie tray lined with parchment, and sprinkling extra chocolate chips on top of the cookies.

How to Make Healthy Chocolate Chip Cookies

In a medium mixing bowl, combine the flour, baking soda and sea salt. In a separate large bowl, whisk together the coconut oil, yogurt, coconut sugar, vanilla and egg. Add the dry ingredients to the wet ingredients and stir until combined. Fold in the chocolate chips. Using a Tablespoon or cookie scoop, drop Tablespoon sized balls of cookie dough onto a cookie sheet lined with parchment paper or a silicone baking mat.

Top with additional chocolate chips and bake at 350ºF for 9-10 minutes or until the edges are slightly browned. The cookies will be very soft coming out of the oven but they firm up after setting so allow the cookies to set for 10 minutes before transferring to a wire rack to cool completely.

pro tip!
Make sure your yogurt and egg are at room temperature otherwise your coconut oil will harden when mixed together. If your coconut oil does harden, make a warm water bath by placing the bowl in the sink or a larger bowl with hot water until the coconut oil melts. 
An overhead photo looking down on healthy chocolate chip cookies on a wire cooling rack.

Variations and Tips

  • Don’t mix the batter too much! When you add the dry ingredients to the wet, stir until just combined and then gently fold in the chocolate chips. If you overmix, the cookies may get to dense and crumbly!
  • If the edges of your cookies are golden brown, they’re done! They will be super soft when you remove them from the oven but I promise they will firm up while they set. Don’t over-bake the cookies!
  • This recipe makes 15 cookies – feel free to double or triple the recipe for a bigger batch!
An overhead photo looking down at a wire cooling rack with healthy chocolate chip cookies scattered around it. A hand is removing one of the cookies from the bottom right hand corner.

FAQs

Can I use all-purpose flour?

Yes! All-purpose flour will work just fine in place of whole wheat pastry flour.

How can I make these cookies gluten-free?

I haven’t tested a gluten-free version of these cookies, but I would imagine using a 1:1 gluten-free all-purpose flour would work just fine in place of the whole wheat pastry flour. My favorite brand is Bob’s Red Mill gluten-free 1:1 all-purpose flour. I also have a recipe for almond flour chocolate chip cookies if you are looking for a gluten-free recipe!

Can I replace the coconut oil?

Feel free to use melted butter or vegan butter in place of the coconut oil. Another neutral oil like avocado or olive oil would also probably work just fine.

How can I make these cookies vegan?

I haven’t tried vegan substitutes, but I would imagine using a vegan yogurt and a flax egg would work just fine. Let me know if you try these substitutes in the comments below!

Can I use a different sweetener in place of coconut sugar?

White sugar would work just fine, but I haven’t tried a liquid sweetener like maple syrup or honey so I’m not sure how that would change the recipe. If you try it, let me know in the comments below!

Four healthy chocolate chip cookies stacked on top of eachother.

Storing and Freezing

After allowing the cookies to cool first on the baking sheet and then completely on a wire rack, you can store the cookies in an airtight container at room temperature for up to 3-4 days. For longer storage, you can refrigerate for up to one week and freeze for up to 3 months. If you freeze the cookies, just make sure you use a freezer-safe container!

Be sure to check out all of the cookie recipes here on EBF.

Healthy Chocolate Chip Cookies

5 from 7 votes
These healthy chocolate chip cookies are soft, chewy and guaranteed to satisfy any sweet tooth. They're made with whole wheat flour, coconut oil, Greek yogurt and coconut sugar. There's no butter and no chilling required!
Three healthy chocolate chip cookies stacked on top of each other. The top cookie has been cut in half, exposing the inside.
Prep Time 10 minutes
Cook Time 10 minutes
Total Time 20 minutes
Servings 15 cookies

Ingredients

Instructions
 

  • Preheat oven to 350°F and line a baking sheet with parchment paper or silicone baking mat.
  • In a medium mixing bowl combine the flour, baking soda and sea salt.
    A mixing bowl with flour, baking soda and sea salt. A hand is using a golden spoon to mix the ingredients together.
  • In a large mixing bowl whisk together the coconut oil, yogurt, coconut sugar, vanilla and egg.
    A mixing bowl with coconut oil, yogurt, coconut sugar, vanilla and egg being whisked together.
  • Add the dry ingredients to the wet and stir until combined.
    Wet ingredients being poured into a mixing bowl with dry ingredients.
  • Fold in the chocolate chips.
    Chocolate chips added to the cookie dough mixture.
  • Using a tablespoon or small cookie scoop, roll the dough into heaping tablespoon sized balls and drop onto the prepared baking sheet. Press cooking dough down slightly into a cookie shape using a spoon or your fingers.
    Balls of cookie dough being flattened with the back of a spoon on a baking sheet lined with parchment paper.
  • Top with additional chocolate chips and bake for 9-10 minutes or until edges are slightly browned.
    A spoon with additional chocolate chips to add more chocolate chips to the tops of the cookie dough that have been portioned out on a baking sheet.
  • The cookies will be very soft coming out of the oven, but they’ll firm up after setting so make sure to allow the cookies to set for 10 minutes before transferring to a wire rack to cool completely.
    Eleven freshly baked healthy chocolate chip cookies on a baking sheet lined in parchment paper.

Video

Notes

  • Whole wheat pastry flour: If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • Coconut sugar: White or cane sugar works as well. I haven’t tried a liquid sweetener in place of the coconut sugar so I’m not sure how the cookies would turn out. 
  • Greek yogurt: I haven’t tried a vegan yogurt substitute, but I would imagine any dairy-free yogurt would work just fine. 
  • Egg: I haven’t tested this recipe with a vegan substitute, so let me know if you try this with a flax egg in the comments below! 

Nutrition

Serving: 1cookie Calories: 129kcal Carbohydrates: 21g Protein: 2g Fat: 6g Saturated Fat: 4g Sodium: 146mg Potassium: 135mg Fiber: 3g Sugar: 8g
Course: Cookies, Dessert
Cuisine: American
Keyword: healthy chocolate chip cookies

DID YOU MAKE THIS RECIPE?

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Recipe Rating




    12 comments
    1. Becky Bender
      February 19, 2022 AT 8:38 am

      What can i use in place of whole wheat flour? I’m gluten free
      Thank you

    2. Janine
      January 14, 2022 AT 12:34 am

      5 stars
      Wow, these are so good! Not too sweet but hit the spot when wanting a treat. This is how you make choc chip cookies for adults. Yum!

      1. Brittany Mullins
        January 14, 2022 AT 3:37 pm

        Yay!! So happy to hear this, Janine. Thanks for the review. It means the world to me!

    3. Katie W.
      January 10, 2022 AT 9:03 pm

      5 stars
      These were such an amazing healthy cookie option! I could hardly tell these weren’t full-fat butter cookies. The whole wheat flour gives it a bit of grainy texture, but I love the flavor it gives. Great healthy alternative for my sweet tooth!

      1. Brittany Mullins
        January 11, 2022 AT 10:55 am

        So thrilled you enjoyed these cookie, Katie. Thanks so much for trying them out and coming back to leave a review. I so appreciate it!

    4. Lisa
      January 9, 2022 AT 8:31 am

      5 stars
      These came out SO good! The only swap I made was I used all
      Purpose flour because I didn’t have the whole wheat pastry flour on hand and they were out at the store but turned out great!! So good and fiancé approved ! He couldn’t tell any difference and came back for seconds ❤️

      1. Brittany Mullins
        January 10, 2022 AT 11:18 am

        Woo!! Happy to hear this cookies were a success, Lisa. Thanks for trying them out and coming back to leave a review!

    5. Kathy
      January 7, 2022 AT 4:33 pm

      Could you recommend a flour that is gluten free I could use for these but without rice flour. I can’t have rice, Almond or oats. Feel stuck for baking. I can’t have wheat.

Parchment paper lined with protein balls.

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