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The Best Healthy Chocolate Chip Cookies

Healthy Chocolate Chip Cookies – After several trial and errors, I can officially proclaim that these are the BEST healthy chocolate chip cookies I have ever made. And my family agrees too (and they are critical of “healthy” anything!).

healthy chocolate chip cookies

Honestly, is there anything better than a warm chocolate chip cookie? Cookies are not only easy to make, but practically foolproof.

I mean, who would not love to eat a chocolate chip cookie?

Right. This. Very. Minute.

What About Healthy Chocolate Chip Cookies?

I am the first to admit that putting the word “healthy” in front of any type of dessert recipe kind of spoils the all yummy fun. But I promise my recipe for healthy chocolate chip cookies will still make you (and the kids!) smile.

Here’s some healthy swaps I made to make these Chocolate Chip Cookies healthy:

SWAP #1: Replace white sugar for coconut sugar

Instead of using refined and empty calorie table sugar, these healthy chocolate chip cookies are sweetened with coconut palm sugar, which is not an empty calorie because it does still contain nutrients and minerals. Although I wouldn’t necessarily classify coconut palm sugar as a “superfood”, it is a much better choice than table sugar! Besides, my cookie recipe only has about 1/2 the amount of sugar you would get from a typical chocolate chip cookie recipe. And yes, it is still plenty sweet.

SWAP #2: Replace brown sugar for coconut sugar + molasses

Brown sugar is what gives most chocolate chip cookies dimension. However, we don’t use sugar for the many health reasons you can find here. But adding just a little bit of molasses does the trick. I add 2 teaspoons of molasses to coconut sugar for every 1 cup of replacement. In this recipe, it only calls for 1 teaspoon to account for the 1/2 cup of brown sugar we are replacing.

healthy chocolate chip cookies

SWAP #3: Replace shortening for coconut oil or real butter

We never want to use shortening — or trans fats. Want to learn more? Read our reasons here. Using coconut oil as a shortening replacement is ideal. However, 100% butter is a great replacement too.

SWAP #4: Replace wheat/white flour for gluten free whole grain flour

We believe in living an anti-inflammatory lifestyle, which means we choose whole grain gluten free flours over the standard wheat flours. Is flour bad for you? It’s not as simple as you think and we wrote about this topic in detail here. Using a gluten free flour substitute is great — even better when it’s whole grain gluten free like King Arthur’s Flour.

How to make the BEST Healthy Chocolate Chip Cookies

We use a little bit of apple cider vinegar in our cookies. Vinegar is a surprisingly common ingredient in baked goods — yes, considering that it has such a sharp flavor to it.

When used in bake goods, vinegar reacts with the baking soda to create a chemical reaction and gives the batter some extra lift.

healthy chocolate chip cookies

Milk With Your Healthy Chocolate Chip Cookies

Oh yes, a glass of tall milk with cookies sounds wonderful, doesn’t it? Well, I can’t give you the BEST healthy chocolate chip cookies recipe without first providing some options for plant-based alternatives to milk.

After all, not only is cow’s milk the most common food allergy, but a whopping seventy-five percent of the world’s adult population also happen to be lactose intolerant.

See our favorite Milk Alternatives here.

You can easily make your own Hemp Milk or Almond Milk to pair with this and if you want them a little sweeter, just add in a big of maple syrup and pure vanilla extract.


Healthy Chocolate Chip Cookies

These are the BEST ever healthy chocolate chip cookies. They are gluten free, dairy free and refined sugar free.

healthy chocolate chip cookies
Save Recipe
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Total Time: 35 minutes
  • Yield: 1218 cookies 1x



  1. Preheat oven to 350 degrees. Line a baking sheet with parchment paper, or use our favorite stoneware baking pan.
  2. In a large bowl, add the coconut oil (or butter) and  coconut palm sugar and beat for 2-3 minutes with a hand mixer or stand mixer. healthy chocolate chip cookies
  3. Next, add the molasses, vanilla, apple cider vinegar (measure carefully!) and egg and mix for another 2-3 minutes.healthy chocolate chip cookies
  4. To the large bowl, add the gluten free flour, baking soda and sea salt. Then, hand mix with a spatula or wooden spoon. I love using the Mix and Stir Scraper — one utensil to mix and scrape the sides of the bowl. healthy chocolate chip cookies
  5. Add in the chocolate chips and nuts (optional). Mix well until all ingredients are well blended. healthy chocolate chip cookies
  6. Using a medium cookie scoop, scoop the cookie dough mixture and place cookies on your baking sheet about 1/2 inch apart. healthy chocolate chip cookies
  7. Bake until the cookies are golden, about 8-10 minutes (do not over bake). If you using a stoneware pan, let cool on the pan for a few minutes before transferring them to a cooling rack.healthy chocolate chip cookies

Last Step! If you loved our recipe, leave us a review below. This helps future recipe makers and ensures continued high-quality recipes for years to come!



For this Healthy Chocolate Chip Cookie recipe, you definitely want the coconut oil to be firm (or cold). For the warmer months, if your coconut oil is liquid, then measure out the amount needed for this recipe and add it to the fridge for about 30 minutes – 1 hour until it’s more solid. Then, when you’re done mixing the dough, place it back in the fridge until it’s more solid and you’re ready to bake – as well as when in between baking trays. It may just take a little bit more effort on your part, but they are definitely worth it.

  • Cookies can be stored in an airtight container for up to 3 days or frozen in a sealed zip-top bag for up to one month.
  • If you don’t have time to cook all of the dough, you can place in the fridge for up to 2 days and cook later.

© 2024 clean cuisine Recipe by:

P.S. Is Your Cookie Pan Toxin-Free?

best non toxic baking sheet

Click HERE to learn more about choosing a toxin-free cookie pan.

Aimee Niedosik

Aimee loves to craft delicious, nutrient-dense recipes to share with her family and friends. While in remission from autoimmune diseases and underlying viruses, she still maintains an anti-inflammatory and anti-aging diet. Aimee is a Christian, website designer, autoimmune community leader and lives in North Carolina with her husband, 2 kids and 2 dogs.

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Saturday 12th of June 2021

I would love to make these, but I am sensitive to coconut! Can you recommend a substitute for the coconut oil and coconut palm sugar?

Aimee Harris Niedosik

Sunday 13th of June 2021

Hi Lauren, The BEST substitute for coconut oil is butter -- so, if you can tolerate butter, then I highly recommend you find some organic, 100% unsalted butter and use that instead. For the coconut sugar swap, I recommend using date sugar since it's the same consistency. If these swaps work for you, let me know!!

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