These are absolutely the best Healthy Chocolate Chip Cookies that are soft, chewy, and loaded with dark chocolate chips. I have perfected my healthier cookie recipe and kids call it “Classic”!

For more healthy cookies with chocolate chips, try these oat flour chocolate chip cookies and almond flour chocolate chip cookies.

Healthy chocolate chip cookies stacked on white plate.

I am extremely picky when it comes to healthy cookies. Cookies gotta be worth their calories!

When I think of healthy chocolate chip cookies, I envision a layer of soft buttery dough covering chocolate chips like a blanket, and when you bite in, the cookies are chewy.

And that’s this recipe!

Why You’ll Love This Recipe

  • Tried and true recipe: This is a very old recipe of mine that I have changed and perfected over the years. The toughest critics, kids, approved!
  • Wholesome ingredients: We use organic cane or coconut sugar, whole wheat or spelt flour with bran and germ attached, and better for you dark chocolate chips.
  • No sacrificing the taste: Unlike many traditional recipes online, our recipe uses twice less sugar and butter, resulting in yet soft and chewy healthy chocolate chip cookie recipe. Plus no banana, applesauce, flax seeds or avocado are involved.
  • Quick and easy: Cookie dough comes together in one bowl and we chill it only for 20 minutes.

Ingredients for Healthy Chocolate Chip Cookies

You will need only 8 simple ingredients to make these healthy chocolate chip cookies.

Whole wheat flour, sugar, salt, vanilla extract, egg, baking soda, chocolate chips, butter.
  • Butter: I used organic salted butter and omitted salt. Unsalted butter works perfectly too.
  • Sugar: I used organic cane sugar. Coconut sugar works too. You can also use all or parts of organic brown sugar as it goes well in chocolate chip cookies. I do not recommend to use liquid sweetener as recipe will not work.
  • Whole wheat flour or spelt flour: This time I used whole grain spelt flour. Please don’t use all-purpose flour, recipe will need adjustment.
  • Baking essentials: Pure vanilla extract, baking soda and salt, if using unsalted butter. No need for baking powder as we do not want cookies to have fluffy texture.
  • Chocolate chips: I use dark chocolate chips because sweetness in a cookie dough is enough already. You can use semi-sweet chocolate chips or Lily’s sugar free chocolate chips and more of, if you like.

How to Make Healthy Chocolate Chip Cookies

Here is a rundown with a few tips how to make healthy chocolate chip cookies. You can find full printable recipe card with ingredients amounts and instructions down below.

Step by step process how to make healthy chocolate chip cookies.
  • Make the cookie dough: In a large bowl, beat softened butter and sugar with an electric mixer. Then add egg and vanilla extract, and then dry ingredients – baking soda, salt and flour. Fold in 1/4 cup chocolate chips and your cookie dough is formed.
  • Chill the dough: Place cookie dough in the freezer to chill for 20 minutes. This is a must to prevent cookies from spreading.
  • Roll and bake: Scoop dough with a regular cookie scoop, roll into balls and place on prepared baking sheets 3 inches apart. Cookies spread, plan for 6 per sheet. Bake cookies for 10 minutes and remove while cookies appear underbaked, puffy and light in color. Dough will settle during cooling.
  • Add more chips: Strategically place remaining 2 tablespoons of chocolate chips into cookies while they are still hot. Also you can skip this step and just add all chips into the dough.
  • Cool: Let cookies cool on a baking sheet for 15 minutes before transferring onto a cooling rack to cool more. As cookies cool, you will see delicious grooves covering chocolate chips like a blanket appearing.

Tips for Best Results

Here are my well-tested tips for the best healthy chocolate chip cookies results!

  • Use cold baking sheets: Make sure your baking sheets are cold. If you baked other cookies right before, cool them off. I stick mine in the fridge for 5 minutes.
  • Measure flour correctly: I can’t stress enough, how important it is! Spoon flour into a measuring cup and level with a butter knife. Do not dip measuring cup into a bag with flour!
  • Use softened butter: Softened butter means a dent appears when you touch it with a finger. To soften butter, just leave it at room temperature for 3-4 hours. To speed up softening, cut up in cubes and let warm up.
  • Do not overmix the cookie dough: Overmixing will make the cookies more prone to falling apart.
  • Don’t skip chilling the dough: Because this cookie dough contains butter and sugar, it has to be firmed up before baking. If you don’t chill the dough, your cookies will spread like crazy!
  • Do not over bake cookies: With most cookies you want to remove them from the oven before they start browning and finish settling during cooling off period. It’s a golden cookie baking rule!
Healthy chocolate chip cookies with one broken in half on a plate.

Variations

  • A cookie sandwich: Kids will love when you turn these healthy chocolate chip cookies into dinky doozies! Just sandwich two cookies with healthy buttercream or healthy chocolate frosting.
  • Coconut oil: You may use coconut oil but it results in more crispy rather than chewy cookies, with less grooves and more cake like looking cookies.
  • Brown sugar: Some love a hint of molasses brown sugar provides. You can sub half the amount of white sugar.
  • Naturally sweetened: Add instead of chocolate chips add raisins or cacao nibs (but less).
  • Coconut flakes: Stir in a few tablespoons of fresh or toasted unsweetened coconut flakes into the cookie dough before chilling it.
  • Nuts: A few tablespoons of chopped peanuts, macadamia nuts, pecans or walnuts will add texture and flavor.
  • Fancy cookies: Chop up dark chocolate bar into chunks and add instead of chocolate chips. Once freshly baked, sprinkle cookie with flaky sea salt while still hot and after intentionally placing the extra chips in.

How to Store

Store: If you like chewy cookies, store in a cool dry place in an airtight container for up to 5 days. If you like crispy cookies, store them in a ventilated container.

Freeze: Bake and cool cookies completely. Then place in a resealable plastic bag or airtight container and freeze for up to 3 months. Thaw on a counter for a few hours.

You can also freeze chocolate chip cookie dough itself or roll into balls, freeze on a baking sheet and and then transfer into the container. Thaw in the fridge overnight before baking. If you decide to defrost them on a counter, you will have to place the balls to chill in the freezer for 20 minutes before baking.

Ship: A batch of chocolate chip cookies is perfect for shipping to family and friends. Bake and cool. Place 2 cookies back to back and wrap with plastic wrap. Then place in a plastic container with a lid, stuffed with tissue, inside the shipping box and voila.

FAQs

Can I use any other flour besides whole wheat flour?

Unfortunately not. Baking is a science and all flours act differently. Recipe has been tested only with whole wheat flour and spelt flour.

Can I use honey or maple syrup instead of sugar?

If you use maple syrup or honey instead of sugar, cookies will come out very cakey. I do not recommend. Sugar and butter melt during baking and create a real cookie experience.

Why my cookies haven’t spread during baking?

Most likely because you haven’t measured flour correctly, so cookies end up more dry as butter absorbs higher amount of flour. Be sure to scoop flour with a spoon into a measuring cup and then level the top with a butter knife.

More Healthy Cookies Recipes to Try

Healthy Chocolate Chip Cookies

These are absolutely the best Healthy Chocolate Chip Cookies that are soft, chewy, and loaded with dark chocolate chips. I have perfected my healthier recipe and kids call it "classic"!
4.95 from 40 votes
Servings 12 cookies
Calories 166
Diet Vegetarian
Prep Time 12 minutes
Cook Time 10 minutes
Chilling and Cooling Time 35 minutes
Total Time 57 minutes

Ingredients  

Instructions 

  • In a large bowl, add butter and sugar; beat with a mixer until creamy.
  • Add egg and vanilla extract, beat until combined. Add baking soda, salt and flour; beat until cookie dough is formed. Add 1/4 cup chocolate chips and stir with spatula.
  • Place cookie dough in the freezer to chill for 20 minutes. In the meanwhile, preheat oven to 350 degrees F and line 2 cookie sheets with unbleached parchment paper or silicone baking mats.
  • Scoop dough with a regular scoop, roll into balls and place on prepared baking sheets 3 inches apart. Cookies spread.
  • Bake for 10 minutes and remove while cookies appear underbaked, puffy and light in color. Strategically place remaining 2 tablespoons of chocolate chips into cookies while they are still hot.
  • Let cookies cool on a baking sheet for 15 minutes before transferring onto a cooling rack to cool more. As cookies cool, you will see delicious grooves covering chocolate chips like a blanket appearing.

Video

Notes

  • Store: If you like chewy cookies, store in a cool dry place in an airtight container for up to 5 days. If you like crispy cookies, store them in a ventilated container.
  • Freeze: Bake, cool cookies completely, place in a resealable plastic bag or container and freeze for up to 3 months. Thaw on a counter for a few hours.
  • Softened butter: Softened butter means a dent appears when you touch it with a finger. To soften butter, just leave it at room temperature for 2-3 hours. To speed up softening, cut up in cubes.
  • Salted butter: If you use salted butter, omit salt.
  • Don’t skip dough chilling: Otherwise your cookies will spread.
  • Flour: Don’t use any other flour except the one instructed in this recipe. Measure flour correctly by scooping it with a spoon into a measuring cup and then leveling with a knife.

Nutrition

Serving: 1cookie | Calories: 166kcal | Carbohydrates: 18g | Protein: 3g | Fat: 10g | Saturated Fat: 6g | Cholesterol: 36mg | Sodium: 127mg | Fiber: 2g | Sugar: 6g
Course: Dessert
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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Comments

    1. I’m sorry to hear this. There could be two reasons why it happened. Either you haven’t measured the flour correctly. You should scoop it with a spoon into a measuring cup and level the top with a knife. Or your oven runs hotter and cookies got over baked and dried out. Bake for less time next time. Hope this helps.

  1. My cookies didn’t flatten. I learned that happens when you add too much flour. I followed the recipe. Did anyone else have this experience? Should I add less flour?

    1. Hi Lilia. How did you measure the flour? You should spoon it into a measuring cup and flatten the top with a knife. If you dipped cup into the bag with flour then yes, you could have too much flour. Did you chill the dough? I do think you used too much flour for some reason, you are correct. What flour was it? And did you use softened butter and sugar?

      1. Thank you for your quick reply! I dipped the cup into the bag, so perhaps I added too much. I used whole wheat flour. I’ll try again using your method! Alternatively, I could weigh the flour.

        1. Sounds good! Just FYI all recipes use “my method” for measuring flour. Just so you know to avoid future fails. It’s a default in baking.

    1. Recipe will need adjustment and I haven’t tested it. You may try with this ratio – Use 1 cup of white flour for every 3/4 cup of whole wheat flour that recipe calls for.

  2. I have found that when I substitute coconut sugar in place of cane sugar I need to add a bit of water to keep the dessert from being too dry. Have you noticed this?

    1. That is possible. Honestly I do not use it often because I need cookies to have “normal” color for photography. I wouldn’t add water but bake for less time.:)

  3. 5 stars
    I made these and they turned out good. I didn’t chill and while they did spread, they were still mostly not touching each other.

  4. 5 stars
    These cookies were the best I’ve made. So chewy and delicious with the perfect amount of sweetness. I’ve tried many recipes, but these are my kids favorite. We are making another batch today.

  5. 5 stars
    My 12 and 14 year old girls were tasked with making these on their own. Your video was so helpful, they followed your exact instructions (unlike when their Mum tries to explain things in the kitchen). They were so amazingly good that the rest of the family have said they now HAVE to cook them at least once a week!)

  6. 5 stars
    So I changed these a bit and they were a big hit. I used a mix of all purpose flour and white whole wheat because I didn’t have whole wheat or spelt, 1/3 cup dark brown sugar, chocolate chunks and raisins and I didn’t chill them. I thought that they would spread but they didn’t. I rolled them into a ball and they spread minimally and came out perfect. Thank you for the recipe. I am always reducing sugar in recipes and it tough to find low sugar, honey or maple syrup cookies.

4.95 from 40 votes (17 ratings without comment)

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