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DIET / Gluten Free / The Best Healthy Chocolate Chip Cookies

The Best Healthy Chocolate Chip Cookies

Dairy FreeGluten FreeVegetarianBy Aimee Niedosik  Published: 10/20/2020  Updated: 05/13/2021
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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.

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Print

Healthy Chocolate Chip Cookies

healthy chocolate chip cookies
Print Recipe

★★★★★

4.5 from 2 reviews

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

  • Author: Aimee Harris Niedosik
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Total Time: 35 minutes
  • Yield: 12–18 cookies 1x
  • Category: Dessert
  • Method: Oven
  • Cuisine: American
  • Diet: Gluten Free

Ingredients

Scale
  • 1 cup coconut oil (firm, not liquid – see notes below)
  • 1 1/2 cup coconut palm sugar
  • 1 teaspoon molasses
  • 2 teaspoons vanilla extract
  • 1 teaspoon apple cider vinegar
  • 1 pastured organic egg, lightly beaten
  • 2 cups of  1-for-1 gluten-free flour mix, such as King Arthur’s
  • 1 teaspoon baking soda
  • 1/4 teaspoon unrefined sea salt
  • 3/4 cup dairy-free dark chocolate chips
  • OPTIONAL: 3/4 cup finely chopped walnuts or pecans

Instructions

  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

Notes

COCONUT OIL NOTES:

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.

Keywords: Healthy Chocolate Chip Cookies

Clean Cuisine Approved:

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

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Cookies, Dairy Free, Desserts, Gluten Free, Nut Free, Vegetarian

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Comments

  1. Lauren says

    June 12, 2021 4:46 PM

    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?

    Reply
    • Aimee Harris Niedosik says

      June 13, 2021 8:26 AM

      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!!

      Reply
  2. Luann says

    April 19, 2021 9:46 PM

    Hi! Can you use almond flour instead of gluten free flour?

    Reply
    • Madison Suttles says

      April 19, 2021 9:56 PM

      Hi, Luann!

      While I’ve never tried subbing almond flour instead of gluten free flour in this particular recipe, it is definitely worth a try! I have tried this substitute in other recipes where the ratio is pretty close to 1;1, but requires either a little less, or a little bit more almond flour to achieve the correct texture. If you try it out, let us know how it goes!

      Hope this helps,
      Madison

      Reply
      • Luann says

        April 20, 2021 9:58 AM

        Thank you! I’ll let you know how they turn out. 😊

        Reply
  3. Ashley says

    May 18, 2020 5:51 PM

    Can I use a flax egg in this? I see there’s already a good amount of flax in these but I’d prefer to make these vegan.

    Reply
    • Aimee Harris Niedosik says

      May 19, 2020 9:02 AM

      Instead of more flax seed, I would suggest applesauce. If you try this out, please let us know how they turn out some future visitors know too! Thank you!

      Reply
  4. Mary Weber says

    December 22, 2016 8:38 PM

    Hi Ivy
    Could you give me an idea of a breakdown of calories and fats etc-nutrient info on these cookies.
    Even a general idea is good.
    I am SO addicted to sweets and I need to find replacements for my health.

    thank you!

    Reply
  5. Barb says

    December 23, 2014 4:05 AM

    Is this a gluten-free receipe?

    Reply
    • Ivy Larson says

      January 6, 2015 6:47 PM

      No Barb, this one is not gluten free because it does have white whole wheat flour in it, however, if you have issues with gluten the biodynamic flour I suggest as a substitute might work because it is free from the herbicide glyphosate (you can read more about this here: https://cleancuisine.com/biodynamic-farming/ ) —however, if you absolutely cannot have gluten then I suggest substituting Bob’s Red Mill brand “All-Purpose Gluten-Free Flour” for the other flour. That should work just fine!

      Reply
  6. C.K. says

    April 27, 2013 3:35 PM

    I see that you often use coconut oil in your recipes. My understanding from the Swank Foundation is that coconut oil is not good for those living with m.s. Could you explain?

    Reply
  7. Carol says

    January 6, 2011 7:25 PM

    I made these for dessert tonight for my kids and they really liked them. They asked what was in them but I knew better than to tell them about the beans! Thanks for a healthy cookie recipe!

    Reply
    • Ivy Larson says

      January 11, 2011 10:00 AM

      Carol – Yes. Sometimes kids just need to know that it tastes good!

      Reply
    • Pamela Gabrielsen says

      May 13, 2021 1:12 AM

      Hi Ivy – I made your Best Chocolate Chip cookies and they are delicious! I had a little trouble with the batter though – because the coconut oil (Nutiva – not Barleans) is liquid at room temp – I had a bit of a time keeping the dough together to shape or roll balls, trouble getting them up off the parchment lined cookie sheet and trouble keeping them together as cookies even after baking! I’m going to try storing them in the fridge and hope they don’t get too hard – but I am wondering if you have any extra help to provide?? Also I added the pinch of sea salt when I added the baking soda but I don’t see that info in the recipe directions?

      ★★★★

      Reply
      • Aimee Harris Niedosik says

        May 13, 2021 8:02 AM

        Oh yes, I should definitely update the recipe card for warmer months. You definitely want the coconut oil to be firm (or cold)… my suggestion if your coconut oil is liquid, to add the amount needed 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 making trays. It may just take a little bit more effort on your part, but they are definitely worth it. Please keep me posted!

        Reply
      • Pamela says

        May 13, 2021 3:47 PM

        Thanks Aimee! The extra info for warmer months is perfect. I did wind up putting the batter in the fridge between trays and that helped a lot. I think I’ve got the hang of it now. Really tasty cookies – well worth the effort. Since you’re updating recipe directions – Sea salt in batter with (Gluten free) flour?? Thanks for everything.

        ★★★★★

        Reply
        • Aimee Harris Niedosik says

          May 13, 2021 4:07 PM

          I should have you start auditing my recipe cards. YES!! Just added… and yes, they are my favorite. Cold dough always bakes better!!!

          Reply

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