If only every relationship could be as safe, affirming, and rewarding as the one we share with Healthy Chocolate Chip Cookies.

Healthy chocolate chip cookies on a tray

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Pillowy soft with melt-in-your-mouth centers and brimming with dark chocolate chips, these healthy cookies are the kind of steady, judgment-free, and encouraging special something we all need.

Need seconds or thirds (and believe me, YOU DO), and these healthy chocolate chip cookies with applesauce will tell you, GO FOR IT.

They’re low calorie, low sugar, and 100% whole grain.

These are also low-maintenance. This easy chocolate chip cookie recipe doesn’t require a mixer or any advance planning.

And if you have a rough day, nothing comforts quite like a warm batch of homemade chewy chocolate chip cookies. They’re the best mood fixer-upper of them all.

While I have quite the lineup of healthy cookie recipes on my site, and I spent months perfecting the World’s Best Chocolate Chip Oatmeal Cookies for my cookbook, I’d managed to neglect the most classic of them all: a perfect healthy chewy chocolate chip cookie recipe.

Like all great love stories, they were worth the wait!

Whole wheat chocolate chip cookies

How to Make Healthy Chocolate Chip Cookies From Scratch

If you are anything like me, when you are craving a chocolate chip cookie, nothing else will satisfy.

Thanks to this cookie recipe’s more wholesome ingredient lineup, you can feel good enjoying one anytime the longing strikes.

Whole grain and made with applesauce, these healthy chocolate chip cookies are one of the healthiest cookies you can eat!

The Ingredients

  • Coconut Oil. These healthy chocolate cookies have no butter; instead, coconut oil makes them soft and chewy.
  • Applesauce. Naturally sweet applesauce adds moisture to the cookies, while keeping them low calorie.
  • Sugar. A combination of dark brown sugar and granulated sugar provides the perfect amount of sweetness. Dark brown sugar also keeps the cookies moist.
  • Vanilla. A cookie must-have! Be sure to use pure vanilla extract.
  • White Whole Wheat Flour. To keep these cookies healthy without sacrificing texture, I used white whole wheat flour. It provides the same nutritional benefits as regular whole wheat flour but is less dense and lighter in flavor.
  • Cinnamon. I love the warmth and coziness that cinnamon adds to the cookies.
  • Dark Chocolate Chips. With antioxidants and less sugar, dark chocolate is a more wholesome mix-in for our cookies. Plus, they’re absolutely scrumptious!

The Directions

An egg being added to wet ingredients
  1. Whisk the wet ingredients together.
Dry ingredients in a bowl
  1. Whisk the dry ingredients together in another bowl.
Batter being stirred in a bowl
  1. Stir the dry ingredients into the wet ingredients.
Chocolate chips being stirred into a bowl
  1. Add the chocolate chips. Chill the dough for at least 1 hour.
Cookie dough balls on a baking sheet
  1. Roll the dough into balls, and arrange them on a parchment-lined baking sheet. Bake at 350 degrees F for 8 to 9 minutes.
Healthy chocolate chip cookies
  1. Let the cookies cool. Finish baking any remaining dough balls. DIG IN!

Do I Have to Chill My Cookie Dough?

Chilling cooking dough, while it does take some advance planning, is necessary for the best-tasting cookies.

  • One hour of chill time allows the fat to solidify and the wet and dry ingredients to incorporate so that your cookies come out chewy and tender.
  • Chilling cookie dough also ensures the cookies don’t spread too much on the baking sheet.

You can keep the dough at the ready in your refrigerator for up to 2 days or freeze it for months.

Gooey whole wheat chocolate chip cookies

Recipe Adaptations

Storage Tips

  • To Store. Keep cookies in an airtight storage container at room temperature for up to 3 days or in the refrigerator for up to 1 week.
  • To Freeze. Freeze baked cookies in a freezer-safe storage container or ziptop bag for up to 3 months. Thaw and enjoy as desired or bake directly from frozen, adding a few minutes to the baking time as needed.
A tray of healthy chocolate chip cookies

Make Ahead Tip

To Refrigerate Cookie Dough: Prepare the cookie dough as directed, then store it in the refrigerator for up to 2 days. Bake as directed.

To Freeze Cookie Dough: Prepare the dough as directed, and lay the cookie dough balls on a parchment-lined baking sheet. Place the baking sheet in the freezer until the cookie dough is frozen solid. Freeze the frozen cookie balls in a freezer-safe ziptop bag or storage container for up to 3 months. Bake from frozen whenever a craving strikes!

What to Serve with Chocolate Chip Cookies

Whole wheat cookies with melted chocolate chips

Recommended Tools to Make this Recipe

  • Baking Sheets. Perfect for making these delicious cookies.
  • Mixing Bowls. These stackable mixing bowls are easy to clean and store.
  • Whisk. My all-time favorite whisk!

The Best Baking Sheets

Baking sheets are wonderful for baking cookies, making sheet pan meals, roasting veggies, and so much more!

Healthy chocolate chip cookies on a tray

Did you make this recipe?

Let me know what you thought!

Leave a rating below in the comments and let me know how you liked the recipe.

Thick in the middle and pleasantly plump in the best possible way, these tender cookies will stay super soft, even days leftover…not that we can keep them around that long!

Healthy Chocolate Chip Cookies Recipe Video

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YouTube video

Healthy chocolate chip cookies on a tray

Healthy Chocolate Chip Cookies

4.67 from 18 votes
These healthy chocolate chip cookies are thick, chewy, and contain no butter! This low sugar, easy recipe satisfies any sweet tooth!

Prep: 15 mins
Cook: 8 mins
Total: 1 hr 23 mins

Servings: 18 cookies


  • 1/3 cup melted coconut oil* cooled to room temperature (measure when it is liquid!)
  • 1/4 cup unsweetened applesauce
  • 1/4 cup dark brown sugar
  • 3 tablespoons granulated sugar
  • 1 tablespoon pure vanilla extract
  • 1 large egg at room temperature
  • 1 ¼ cups white whole wheat flour or regular whole wheat flour**
  • 1/2 teaspoon baking soda***
  • 1/2 teaspoon ground cinnamon
  • ¼ teaspoon kosher salt
  • 1/2 cup dark chocolate chips plus additional for baking


  • In a large bowl, whisk together the coconut oil, applesauce, brown sugar, granulated sugar, and vanilla extract. Then, whisk in the egg, stopping as soon as it is blended.
  • In a separate bowl, whisk together the flour, baking soda, cinnamon, and salt.
  • Add the dry ingredients to the wet ingredients. With a rubber spatula, stir to combine, stopping as soon as the dry ingredients disappear. The dough will seem very stiff and dry at first. Use the spatula to gently push and "smush" the dough and stir and fold as needed. It will come together.
  • Fold in the chocolate chips. Chill the dough for at least 1 hour, or press plastic over the top and chill for up to 2 days.
  • When ready to bake, preheat the oven to 350 degrees F. Line a baking sheet with parchment paper.
  • With a cookie scoop or spoon, portion the dough, then use your hands to roll into balls that are 1 ½-inches in diameter (you should have 18 total). Arrange on the baking sheet, leaving at least one inch between each. Place any uncooked dough balls that do not fit on the sheet in the refrigerator to continue chilling while the first batch bakes.
  • Bake for the cookies for 8 to 9 minutes, until very lightly browned around the edges and feel dry on the sides and top when lightly touched. They will still appear underdone in the centers. Do not over bake or the cookies will be dry. The cookies will not spread much as they bake.
  • Place the baking sheet on a wire rack and let the cookies cool on the sheet for 2 minutes. Carefully remove the cookies to the rack to finish cooling completely. The cookies will be fragile at first but will firm up and their texture will improve as they cool. Repeat with the remaining dough balls, cooling the sheet completely between batches. Enjoy!


  • *I do not recommend any other kind of oil for this recipe; it’s important that the oil is solid at room temperature (the way coconut oil is) in order for the cookies to set up properly. I haven’t experimented yet, but I believe you could use unsalted butter instead.
  • **If using regular whole wheat flour, the cookies will have a heartier texture and more pronounced “wheat” taste compared to white whole wheat flour. If using regular whole wheat, I recommend a blend of half all-purpose flour and half regular wheat flour. Be sure to measure your flour correctly (lightly spoon it into the measuring cup, then level it off). If you pack the flour too tightly, the cookies will come out dry. Better yet, try weighing the flour.
  • ***Make sure your baking soda is fresh (not expired) or your cookies may not rise and could have a strange aftertaste.
  • To Store. Keep cookies in an airtight storage container at room temperature for up to 3 days or in the refrigerator for up to 1 week.
  • To Freeze. Freeze baked cookies in a freezer-safe storage container or ziptop bag for up to 3 months. Thaw and enjoy as desired or bake directly from frozen, adding a few minutes to the baking time as needed.


Serving: 1(of 18)Calories: 116kcalCarbohydrates: 14gProtein: 2gFat: 6gSaturated Fat: 5gTrans Fat: 1gCholesterol: 9mgPotassium: 52mgFiber: 1gSugar: 7gVitamin A: 15IUVitamin C: 1mgCalcium: 25mgIron: 1mg

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at wellplated.com and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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  1. Used butter because I’m not a fan of the coconut oil taste in cookies. Also subbed xylitol for sugar. Love the flavor and texture.5 stars

    1. Hi Jackie! So glad you enjoyed the recipe! Thank you for this kind review and feedback on substitutions!

    1. I’m sorry to hear the recipe wasn’t to your taste, Steve. I know it’s disappointing to try a new recipe and not enjoy it, so I truly wish it would have been a hit for you.

  2. These are delicious and my new favorite cookies! I made them exactly like the recipe but just left out the cinnamon.5 stars

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