clean eating chocolate chip cookies recipe

Clean Eating Chocolate Chip Cookies

I’ve been experimenting with clean eating chocolate chip cookies for a while because, well, everyone likes chocolate chip cookies.

They are simple, timeless, and just delicious!

I LOVE chocolate chip cookies and cookie dough. I make them often enough, I decided I need a healthier version with better ingredients.

These clean eating chocolate chip cookies hit the spot and satisfy my cookie craving. My family liked them too!

healthy clean eating cookies

These healthy clean eating chocolate chip cookies…

  • Have ZERO processed sugar. (Sweetened with honey and stevia!)
  • Have whole wheat flour instead of white flour. (Organic is best!)
  • Uses coconut oil instead of margarine. (You could also use grass-fed butter for a more classic cookie taste.)
  • Are soft, chewy, and YUMMY!
healthy eating grocery list

Hope you enjoy them!

Check out all my other recipes here. 

healthy chocolate chip cookies

Clean Eating Chocolate Chip Cookies


  • 1 C coconut oil softened ( If you don’t like the taste of coconut oil, use organic grass fed butter)
  • 1/3 C honey (you could also try organic maple syrup)
  • 2 eggs (organic or pasture raised)
  • 1 1/2 C whole wheat flour (organic if possible) You can use half white half whole wheat if desired.
  • 3/4 C dark chocolate chips (I like GHIRARDELLI® or HU Kitchen)
  • 1 scoop vanilla protein powder  (this adds sweetness!)
  • 1 tsp baking soda
  • dash of salt
  • Liquid stevia if you need it to be sweeter. Start with just a drop, it’s stronger than sugar! You can also try coconut sugar or just a bit of organic brown sugar too.


  • Preheat oven to 350°
  • Cream coconut oil, honey and eggs
  • Add protein powder, flour, baking soda and salt, mix well
  • Add stevia if desired
  • Fold in chocolate chips
  • Spoon onto parchment lined baking sheet (makes about 15)
  • Bake for 8 mintues

You Just Can’t Go Wrong With Chocolate Chip Cookies. 

What’s your favorite way to eat cookies? Freshly baked? With a glass of milk? Warmed up and slighly melty? 

I’m drooling just thinking about it. Better go warm up my oven right now and make another batch! 

Enjoy these tasty cookies, let me know what you think about them in the comments! 


  • C J

    So you have to use the protein powder or is there any substitute?
    I don’t have any plus I’ve tried it in other recipes and I could taste it and did t like it

    • Amy

      You don’t have to add protein powder, but I highly recommend it. It adds some extra sweetness and flavor! If you can taste it in other recipes, you could try a different brand of protein.

  • Heather

    What do you think the calorie count is on these per cookie? I followed the recipe minus the stevia. They were delicious! A little oily, but everyone loved them!

    • Amy

      Most traditional cookie recipes call for one cup (or two sticks) of butter. I wanted them to be as close to the original as possible! If you don’t like coconut oil, I’d recommend grass-fed organic butter.

    • Amy

      Hi! If using granulated stevia, start with a small amount (maybe 1 tbsp) and taste to see if it has the desired taste or sweetness. If using coconut sugar, organic cane sugar, or brown sugar, again start with a smaller amount (maybe 2 tbsp) and taste. Stevia has a more bitter after taste so I don’t like to use a ton of it, but it can give it just a bit more sweetness. Hope that helps!

    • Amy

      Personally I like to look for brands that have as simple and minimal ingredients as possible. Like just cocoa, cocoa butter, sugar and that’s about it. I also prefer dark chocolate over milk. GHIRARDELLI® has a 60% cocoa chocolate chip that’s pretty simple and HU Kitchen also has some very clean chocolate chip options!

  • Jaiden

    I didn’t add protein powder or extra stevia and they are not sweet at all. I added 2 additional tablespoons of honey but they are still not sweet. They also pancaked out on my cookie tray vs. the picture where they’re pretty tiny and compact. Might try again and add way more sweetener!

    • Amy

      Protein powder is a key ingredient! It will help sweeten the cookies quite a bit (depending on the brand) and it will help make them more fluffy and compact.

  • Sarah

    Hi! I did the same for everything except i used almond flour.. my cookies went flat when I cooked them. Any ideas of why that happens? And how to prevent that for next time? Thank you!

    • Amy

      Almond flour is much more dense than other flours so it can be tricky to do a 1:1 swap. You could try mixing the almond flour with another flour or you could try chilling the dough before baking. (this sometimes helps regular cookies not go flat)

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