A soft, chewy cookie recipe that beats them all! This is truly the best recipe for Healthy Chocolate Chip Cookies made with coconut oil, natural sugar, whole wheat flour and dark chocolate chips. If you're like me, you will hide these in the pantry from your kids!

I'm a prolific buyer of coconut products, and by that, I mean all the coconut products. In my cart, you will find: coconut oil, coconut sugar (to make my coconut sugar cookies), coconut milk (both canned and fresh), and coconut cream.
I've been buying all the coconut oil to make batches of these healthy chocolate chip cookies for my friends, family, and neighbors. This is one of my favorite easy cookie recipes and because I can have cookies in less than 20 minutes, I tend to make it often. Plus, it only has 8 easy ingredients that you probably already have in your pantry!
Healthy Chocolate Chip Cookie Recipe Ingredients
- Coconut Oil. Today, we're baking with unrefined coconut oil, which means it has not been stripped of its coconut flavor. When you open the jar of coconut oil, it will smell of luscious coconuts and faraway beaches. Refined coconut oil has had the aroma removed so that it can be used for frying without imparting its coconut flavor. It's best if the coconut oil is solid, not melted, because we're going to cream it like we would cream butter for our tea cakes recipe.
- Coconut Sugar. Coconut sugar is also known as coconut palm sugar. It's similar to raw sugar, and it is made by collecting the sap from the coconut flower and then heating to remove excess liquid. It appears like a finer-grain brown sugar. See below for sources and tips to locate coconut sugar.
- Egg Yolk. We only need the egg yolk, not the whole egg for this recipe.
- Vanilla Extract. Real, pure vanilla extract is best here, because it compliments the flavors of the dark chocolate chips.
- White Whole Wheat Flour. My go-to for ensuring my kids eat whole grains made from the entire wheat kernel is white whole wheat flour. It's made from a softer variety of white wheat, so it feels more like regular refined all-purpose white flour, yet it actually is a whole grain. It has all the benefits of using whole wheat flour, but a much milder taste, more similar to regular flour. If you can't find it, use half whole wheat flour and half regular white flour.
- Baking Soda and Baking Powder.
- Dark Chocolate Chips. The darker the chocolate, the better, am I right? I reach for the 72% dark chocolate chips, but I have also used 60% dark. You can also chop up a dark chocolate bar. This will result in much more melty chocolate than using chocolate chips.
Helpful Equipment when making Healthier Chocolate Chip Cookies
- Small Cookie Scoop - This is the best small cookie scoop I have in my kitchen.
- Best Cookie Sheet - I prefer light metal cookie sheets that are not insulated with air or overly thick. This is my current favorite.
Coconut Sugar Chocolate Chip Cookies Substitutions
- Coconut Oil - I don't recommend substituting coconut oil with butter or any other type of oil for this healthy chocolate chip cookies recipe. Coconut oil has a higher percentage of fat solids than anything else, and this recipe has been developed based on that.
- Coconut Sugar - You can use granulated white sugar in place of coconut sugar here. Do not use brown sugar in its place, even though it is the same color. It contains molasses, which changes the moisture of the dough. I talk about this in my Chocolate Chip Cookies without Brown Sugar recipe.
- Flour - I prefer white whole wheat flour for this recipe. This is because it is a whole grain flour that contains all the benefits of using the whole wheat kernel. It is made from a soft white wheat berry so it is not as coarse or harsh as regular whole wheat flour. In the absence of it, use half regular whole wheat flour and half regular all-purpose flour.
Healthy Chocolate Chip Cookies add ins and Variations
Instead of chocolate chips, you can use dried fruit, like dried cranberries or dried cherries. These cookies would be great with ¼ cup of finely chopped pecans in the dough, too. You can also double this recipe successfully, as long as you follow it exactly. This means use two egg yolks (not one whole egg).
How to make Healthier Chocolate Chip Cookies
Preheat the oven to 375, and have a thin light metal baking sheet ready. You can line it with parchment, bake on a silicone mat or spray the cookie sheet lightly with cooking spray to ensure the cookies do not stick.
Next, beat the solid coconut oil and coconut sugar together using an electric hand mixer until creamy. Add the egg yolk and vanilla and beat again.
Finally, add all of the dry ingredients: sprinkle the flour, baking soda, baking powder, and salt evenly over the surface of the wet ingredients in the bowl. Beat everything together until combined.
Lastly, stir in the chocolate chips by hand.
To evenly divide the dough, press it flat in the bowl. Use your eye to divide it into quarters and then make two cookies from each quarter of the dough. Yes, this is a small batch recipe and only makes 8 cookies. You can double it to make more cookies, if you like.
Next, space the cookies evenly on your cookie sheet and press them slightly flat before sliding them into the oven to bake for 9-11 minutes. When the edges of the cookies start to turn golden brown, remove them from the oven. Let cool on the baking sheet for 2 minutes to continue cooking, and then immediately move them to a wire rack to cool completely.
Storing and keeping these Healthy Chocolate Chip Cookies Fresh
Truthfully, these cookies do not last long in our house. I leave them on the counter, lightly covered with a kitchen towel. They will keep an air-tight container for up to 3 days on the counter at room temperature.
I do not recommend making and freezing the dough, because the melting point of coconut oil is so low (just slightly above room temperature), so the oil can melt and ooze out before the rest of the dough defrosts in the oven.
However, you can bake the cookies fully and then freeze them flat in storage bags. Just defrost at room temperature for a few hours, and they're ready to eat.
Can Coconut Sugar Chocolate Chip Cookies be frozen?
These cookies can be frozen if they are already baked. Individually wrap them in plastic and store inside a freezer-safe container. They will keep for up to 3 months. To enjoy, defrost at room temperature for a few hours, and microwave for 5 seconds, if desired. I do not recommend freezing this dough, because if baked from frozen, the coconut oil might seep out before the rest of the dough defrosted.
Frequently Asked Questions about Healthy Chocolate Chip Cookies
The coconut oil, coconut sugar, dark chocolate and whole wheat flour make these different from my traditional small batch chocolate chip cookies. However, they taste just as good as regular cookies!
You can look in the recipe card for the full nutritional information. Personally, I love that these healthy chocolate chip cookies contain a more natural sugar, coconut oil instead of butter, a whole grain, and chocolate with a higher percentage of cocoa solids and antioxidants.
Usually, when we think of healthy, we think of oatmeal. If your idea of healthy chocolate chip cookies must contain oatmeal, jump over to my recipe for Small Batch Oatmeal Chocolate Chip Cookies.
In my kitchen, we can never have enough variations of chocolate chip cookie recipes. I love to make them with coconut sugar, I like to make them with a little espresso powder, I like to make them with oatmeal, and I like to make them with malted milk powder. Just type in the search bar at the top "chocolate chip cookies" and you'll find an extensive list of variations on a classic.
More Favorites from Dessert for Two
Coconut Oil Chocolate Chip Cookies
A small batch of healthy chocolate chip cookies made with coconut oil, naturally sweetened with coconut sugar, and whole wheat flour.
Ingredients
- ¼ cup solid coconut oil
- ½ cup coconut sugar
- 1 large egg yolk
- ¾ teaspoon vanilla extract
- ½ cup white whole wheat flour
- ¼ teaspoon salt
- ¼ teaspoon baking soda
- ¼ teaspoon baking powder
- ¼ cup dark chocolate chips
Instructions
- Preheat the oven to 375. Lightly spray a cookie sheet with cooking spray.
- In a medium bowl, add the solid coconut oil and coconut sugar, and beat until fluffy about combined, about 30 seconds.
- Add the egg yolk and vanilla, and beat until combined.
- Next, evenly sprinkle the flour, salt, baking soda and baking powder on top of the coconut oil mixture. Beat to combine everything well.
- Finally, stir in the chocolate chips.
- Press the dough flat in the bowl (as best you can), and roughly divide the dough in quarters. From each quarter, make 2 cookies, for a total of 8 cookies.
- Space the cookies evenly on the baking sheet, and press them down slightly--not totally flat.
- Bake for 9-11 minutes, until the edges are starting to turn golden brown.
- Let cool on the baking sheet for 2 minutes, and then move to a wire rack to cool completely. (But seriously: who actually lets cookies cool? I eat these straight out of the oven).
Notes
Coconut Oil - Do not substitute coconut oil with butter or any other type of oil. Coconut oil has a higher percentage of fat solids than most other oils.
Coconut Sugar - You can use granulated white sugar in place of coconut sugar here, however do not use brown sugar in its place, even though it is the same color. It contains molasses, which changes the moisture of the dough.
Flour - I call for white whole wheat flour for this recipe. This is because it is a whole grain flour that contains all the benefits of using the whole wheat kernel. It is made from a soft white wheat berry so it is not as coarse or harsh as regular whole wheat flour. In the absence of it, use half regular whole wheat flour and half regular all-purpose flour.
Storage: They will keep an air-tight container for up to 3 days on the counter at room temperature. I do not recommend making and freezing the dough, because the melting point of coconut oil is so low (just slightly above room temperature), so the oil can melt and ooze out before the rest of the dough defrosts in the oven. However, you can bake the cookies fully and then freeze them flat in storage bags. Just defrost at room temperature for a few hours, and they're ready to eat.
Nutrition Information:
Yield:
8Serving Size:
1Amount Per Serving: Calories: 178Total Fat: 10gSaturated Fat: 7gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 47mgSodium: 132mgCarbohydrates: 21gFiber: 1gSugar: 15gProtein: 2g
Jen says
Hi hi. I followed your recipe and the dough was super sticky. Should I have added more flour? Thanks!!
Christina Lane says
Hmmm...I'm not sure why. Did you change anything by chance? If it happens again, I usually just opt to chill recipes before baking instead of adding more flour.
Nick says
In what world is a baked-goods recipe called HEALTHY in which Anything coconut is used, much less loaded up?? The words "Sat fat" and "healthy" are never put into the same sentence by any nutritionist. Delicious perhaps, decadent for sure, but never, ever healthy. Who's fooling with words?
Suzanne says
These are the best healthy choc chip cookies I have ever tried. I substituted grass fed butter because I didn’t have coconut oil. So good! I also did 1/4 white flour and 1/4 almond flour and they are delicious! Thank you for this recipe!
Sammtha says
Would you have an egg replacement for this recipe?
Christina Lane says
Have you ever made a flax egg?
Shea Lane says
I came across this recipe and immediately got SUPER happy, as I am a health nut, but I love me a good chocolate chip cookie 😩 I also want our 11 month old daughter to be able to enjoy “sweets” to an extent. I have been very strict with our child thus far and I’m known as the “mean mom” because I allow bare minimums of sugar. Unfortunately though, I am also concerned with saturated fat. It seems as though this recipe has a high amount of saturated fat per serving, that is upsetting ☹️ How many cookies are in a serving? Because if it is only 1 then I’d say these cannot truly be “healthy” due to the high content of sat. fat.
Ruby says
This type of saturated fat is a necessity for our bodies, and because *i hope* you're not eating the whole batch of cookies in one sitting, the amount of good, heart healthy fat from the UNREFINED coconut oil can benefit your body and is very healthy.
Lynn Amy says
Generally, cooling cookie dough in the fridge for 30 minutes before you bake cookies will keep them from falling flat.
Kelly says
Hi! Have you or do you think Stevia would work in this recipe? I made them with coconut sugar and they were amazing! Just curious as I have a pre-diabetic in my life. Thank you! Kelly
Christina Lane says
Hi Kelly,
Hmm..I'm not sure. Does the stevia package have any instructions on the back that says it's a 1:1 ratio for substitution?
Jane says
I just made these for a friend who had a baby. I had to substitute brown sugar for coconut (only thing I had on hand & was in a time crunch) but they turned out great!
Abby says
I Loved these cookies... I've been loving adding ground flax seed, so I substituted 2 Tablespoons of flax into the amount of flour, which was spot on! I loved them!
Chris Reilly says
I can't wait to try these! I think I'll add in some shredded coconut (unsweetened because that's what I have in my freezer) AND pecans! Thanks for always making treats in smaller batches Christina!! 💜