The best Healthy Chocolate Chip Cookies! Made with whole wheat flour, these soft cookies are delicious and made with wholesome ingredients! This post is sponsored by my friends at Hu Kitchen.

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There are few things better than a warm chocolate chip cookie. Soft centers, melty chocolate, crispy outside…. YUM!
Most chocolate chip cookies are high in fat, calories, and sugar – and while being totally delicious, they’re definitely not a ‘health’ food.
This Healthy Chocolate Chip Cookie Recipe is perfect for those who want to indulge mindfully.
Why we love these Whole Wheat Chocolate Chip Cookies
There’s a lot to love about these chocolate chip cookies (I mean really.. what’s not to love about a warm chocolate chip cookie!) Here’s why we love them:
- Simple Ingredients – These cookies are made with only 8 simple ingredients that you probably already have on hand.
- Loaded with chocolate – We did not skip on the chocolate in these cookies. They’re loaded with our favorite Hu Kitchen Gems!
- Lighter than a regular cookie – These chocolate chip cookies are lighter than your standard chocolate chip cookies with fewer calories, sugar, and fat.

Whole Wheat Flour vs. Regular Flour Cookies
Whole wheat flour and regular flour cookies are a little bit different. With whole wheat flour you can taste the flour a bit more (a little bit more earthy) and it gives the cookies a bit of a denser texture.
You can substitute regular white flour in place of whole wheat flour if you’d like!
If you’re looking for a regular chocolate chip cookie – check out this recipe for Double Chocolate Chip Cookies!
Ingredients for Whole Wheat Chocolate Chip Cookies
To make these whole wheat chocolate chip cookies you’ll need:
- white whole wheat flour -white whole wheat flour is lighter than regular whole wheat flour which gives these a soft center and chewy middle!
- baking soda
- salted butter
- brown sugar
- unsweetened apple sauce
- egg
- vanilla extract
- Hu Kitchen Gems
Here are some of our favorite baking tools that might be helpful for you: baking sheet, parchment paper, spatula, cookie scoop
You can find substitutions for all of these ingredients below in the green shaded substitutions box.

We used our favorite Hu Kitchen Dark Chocolate Gems in this recipe, which are seriously the best for baking!
Hu Kitchen’s Gems are made with only 3 ingredients: organic cacao, organic unrefined coconut sugar, organic fair-trade cocoa butter.
I’ve always been a fan of their chocolate bars, but I think these Gems are even better for baking. They’re so smooth, rich, and melt beautifully – making them the perfect mix in for these healthier chocolate chip cookies!
If you haven’t tried Hu Kitchen – you should! All of their products are vegan, organic, paleo, and soy free. You can use our code CLEANEATING for 15% off site wide.
How to make Chocolate Chip Cookies with Whole Wheat Flour
Making Whole Wheat Chocolate Chip Cookies is very simple! Here’s how we make them:
- Mix the flour and baking soda together in a bowl and set aside.
- Cream together the butter, brown sugar and applesauce. Mix for about 3 minutes to make sure it’s combined well. Add in the egg and vanilla extract.
- Add in the flour mix with the mixer running ¼ cup at a time. Make sure to not over mix- mix only until it’s combined!
- Fold in the chocolate chunks with a spatula.
- Scoop the cookies into 1.5 tablespoon balls – leave about 2 inches for them to spread.
- Bake the cookies for 8-9 minutes. When you take the cookies out they should be a little underbaked. Don’t overbake them.




Pro tip: If you aren’t eating these fresh out of the oven, pop them in the microwave for 5-10 seconds so the chocolate gets super melty. SO yummy!
SUBSTITUTIONS FOR HEALTHY CHOCOLATE CHIP COOKIES
Sadly we do not recommend most substitutions in this recipe. Healthy baking is a science and hard to make changes to! We tested this recipe 3 times and found that this ingredient combo worked best.
Flour: We do not recommend substituting the white whole wheat flour. Homemade Oat Flour or gluten free oat flour will work but will result in a drier cookie with a completely different texture. You could use white all purpose flour if you like. If you’re looking for a yummy gluten free cookie try these Healthy Oatmeal Raisin Cookies or Almond Flour Oatmeal Cookies
Make sure to use white whole wheat flour and not regular whole wheat flour because you will get a much denser cookie. Almond flour and coconut flour will not work and can never be substituted 1:1 for whole wheat flour.
Butter: We do not recommend substituting butter in this recipe. It is essential for the chewy cookie texture!
Brown Sugar: We don’t recommend substituting brown sugar for coconut sugar or other types of sugar in this recipe. Brown sugar is essential for the flavor, texture and these chocolate chip cookies baking correctly.
Applesauce: We haven’t tried substituting applesauce for another ingredient but I think banana or even pumpkin puree would work.
Egg: Substituting with a flax egg will not work
Chocolate Chips: I like to use the Hu Kitchen Gems in this recipe, but you could also use their dark chocolate chips or chopped dark chocolate. Any chocolate chips will work.
Healthy Chocolate Cookie FAQ
Yes, you almost always need to line the baking pan when making cookies. Cookies can easily stick to a baking sheet, especially chocolate chip cookies because the chocolate can melt. Parchment paper or silicone baking liners make for an easy clean up and avoid stuck cookies!
If your cookies are flat it is likely because your butter was too soft or melted. Softened butter should still hold its shape, it shouldn’t be liquified
There are 18 grams of crabs in Chocolate Chip Cookies with Whole Wheat flour.
Wheat flour helps cookies to be fluffy, chewy and gives them a sweet earthy flavor. It also adds whole grains to what is usually a fairly non-nutritious treat.
Most chocolate chip cookies aren’t ‘healthy’ for you but this whole wheat chocolate chip cookie recipe is better for you! It’s lower in fat, calories, and sugars than most cookie recipes while still having great flavor and texture.
Homemade chocolate chip cookies are healthier than store bought cookies for many reasons. Most store bought cookies have added preservatives and funky ingredients to keep them shelf stable. Homemade cookies are made with only real ingredients!

Is it better to use oil or butter in chocolate chip cookies?
It’s always best to use butter in cookies. Butter results in a rich, chewy and crispy cookie, while oil can lead to a cake-like texture of cookies
How Long Do Healthy Chocolate Chip Cookies Last For?
These Whole Wheat Chocolate Chip Cookies will last for up to 5 days on the counter. (If you don’t eat them all before then!)
We recommend storing them in an airtight container to maintain freshness.

How Do You Store Whole Wheat Chocolate Chip Cookies?
Storing: It’s best to store whole wheat chocolate chip cookies in an airtight glass container. These cookies will last for up to 5 days at room temperature but will last even longer if refrigerated.
Freezing: These healthy chocolate chip cookies freeze perfectly! You can freeze the baked cookies in an airtight container or freezer storage bag for up to 3 months.
Freezing the dough: You can also freeze the cookie dough. Once you’ve scooped the cookies onto the baking sheet, pop the sheet in the freezer for 30 minutes. Once frozen, transfer the dough balls to a container or freezer bag. The cookie dough can stay frozen for up to 3 months. When ready to bake, take out the cookie dough and let it sit at room temperature for 10 minutes before baking.
Other healthy dessert recipes:
We love healthier desserts! Here are some of our favorite lower calorie dessert recipes. If you’re looking for other treats check out these Healthy Christmas Recipes or 50+ Healthy Dessert Recipes:
Don’t forget, you can get 15% off all Hu Kitchen products with code CLEANEATING!

Healthy Whole Wheat Chocolate Chip Cookies
Ingredients
- 1.5 cups white whole wheat flour *Do not pack the flour. Scoop, then level off.
- ½ teaspoon baking soda
- ½ stick salted butter softened (4 tablespoons)
- ½ cup brown sugar
- ¼ cup unsweetened apple sauce
- 1 egg
- 1 teaspoon vanilla extract
- ½ cup Hu Kitchen Gems
- Optional – sprinkle sea salt on top when finished baking.
Instructions
- Mix the flour and baking soda together in a bowl and set aside.
- Cream together the butter, sugar and applesauce. Mix for about 3 minutes to make sure it’s combined well.
- Add in the egg and vanilla extract.
- Add in the flour mix with the mixer running ¼ cup at a time. Make sure to not over mix- mix only until it’s combined!
- Fold in the Hu Kitchen Gems with a spatula.
- Preheat the oven to 350 degrees and line a baking sheet with parchment paper
- Scoop the cookies into 1.5 tablespoon balls – leave about 2 inches for them to spread.
- Bake the cookies for 8-9 minutes. When you take the cookies out they should be a little under baked. Don’t over bake them.
- Pro tip: for those perfectly round bakery cookies – as soon as you take them out of the oven hold them about a foot off the counter and drop them. Yes I said drop them . This will deflate them a bit and give you that more round cookie.
- Let them rest on the cookie sheet for 3 minutes then move to a wire rack to continue cooling .
- Store extra cookies in an airtight container for 3-4 days. You can also scoop the cookie dough and freeze it for later.
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