Healthy Chocolate Chip Cookies
Published Jan 07, 2022, Updated Jun 08, 2023
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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!
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!
- 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.
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.
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!
Yes! All-purpose flour will work just fine in place of whole wheat pastry flour.
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!
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.
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!
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!
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!
More Cookie Recipes to Try
- Birthday Cake Cookies
- Chocolate Chip Cookie Skillet
- Almond Crescent Cookies
- No Bake Cookies
- Cottage Cheese Cookies
- Thumbprint Cookies
- Snowball Cookies
- Almond Butter Espresso Cookies
- Almond Flour Cookies
- Peanut Butter Cookies
- Chocolate Peppermint Cookies
- Lemon Almond Flour Cookies
- Healthy Oatmeal Chocolate Chip Cookies
- Peanut Butter Oatmeal Cookies
- Almond Cookies
- Lemon Ricotta Cookies
- Chocolate Crinkle Cookies
- Oatmeal Scotchies
Be sure to check out all of the cookie recipes here on EBF.
Healthy Chocolate Chip Cookies
- 1 ¼ cups whole wheat pastry flour
- 1 teaspoon baking soda
- ½ teaspoon sea salt
- ¼ cup coconut oil, in a liquid state
- ¼ cup Greek yogurt, at room temperature
- ½ cup coconut sugar
- 1 teaspoon vanilla extract
- 1 egg, at room temperature
- ½ cup dark chocolate chips, plus more for topping
- 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.
- In a large mixing bowl whisk together the coconut oil, yogurt, coconut sugar, vanilla and egg.
- Add the dry ingredients to the wet and stir until combined.
- Fold in the chocolate chips.
- 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.
- Top with additional chocolate chips and bake for 9-10 minutes or until edges are slightly browned.
- 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.
- 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 information is automatically calculated, so should only be used as an approximation.
Can gluten-free flour or oat flour be used
If you’re looking for a gluten-free version, I would try 1:1 all-purpose flour vs. oat flour. The oat flour might change the consistency of the cookie too much and I haven’t tested it so I’m not 100% sure what the end result would be.
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.
It looks like this Bob’s Red Mill gluten-free all-purpose flour doesn’t have rice flour in it!
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 ❤️
Woo!! Happy to hear this cookies were a success, Lisa. Thanks for trying them out and coming back to leave a review!
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!
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!
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!
Yay!! So happy to hear this, Janine. Thanks for the review. It means the world to me!
What can i use in place of whole wheat flour? I’m gluten free
Hi, Becky! I haven’t tried it, but you could substitute with gluten-free flour like Bob’s Red Mill Gluten Free 1 to 1 baking flour.