Clean Eating Chocolate Chip Cookies Recipe (2024)

ByTiffany McCauley

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These chocolate chip cookies are perfect for your sweet cravings!

Far be it from me to try and ruin anybody’s eating plan. But every once in a while, it’s nice to splurge and know you haven’t destroyed your plan completely. Am I right? I mean, if you can splurge and still call it “clean”, isn’t that better than drowning yourself in a bunch of “unclean” foods?

Clean Eating Chocolate Chip Cookies Recipe (1)

So I got a little creative. You see, my favorite cookie in the whole wide world is a chocolate chip cookie. What’s not to love? All that melty chocolaty goodness right out of the oven with a tall glass of milk… oh boy. I’m drooling. Pardon me while I go get a napkin.

There. All better.

Now, I have to tell you that I’m particularly proud of these cookies. Why? I wasn’t sure they were going to work when I first put them in the oven. I started with the recipe I used for Clean Eating Cookie Dough a while back. It was never meant to be baked. But with a couple minor adjustments, it did just fine!

Note: You will probably want to double this recipe due to the small yield. However, if you are just baking for yourself and maybe one other person, the yield should be just fine.

More Healthy Cookie Recipes

  • Spelt Chocolate Chip Cookies Recipe
  • Peanut Butter Cookies Recipe


Clean Eating Chocolate Chip Cookies Recipe (3)

Chocolate Chip Cookies

These delicious chocolate chip cookies are certain to satisfy your sweet tooth!

1.75 from 4 votes

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Course: Dessert

Cuisine: American

Prep Time: 30 minutes minutes

Cook Time: 20 minutes minutes

Total Time: 50 minutes minutes

Servings: 1 batch

Calories: 1301kcal


  • cup almonds
  • cup cooked oatmeal (cooked and fully cooled)
  • 3 tbsp. honey
  • 1 tsp. pure vanilla extract
  • 1 tsp. ground cinnamon
  • cup whole wheat pastry flour
  • ½ cup dark chocolate chips (I use Lilly's or EnjoyLife)

US Customary - Metric


  • Preheat oven to 325 degrees F.

  • Mix everything except the chocolate chips in a food processor. You should have a nice wet, sticky dough when you're done.

  • Using your spatula, scrape dough into your mixing bowl and mix in chocolate chips.

  • Spoon onto a parchment lined cookie sheet.

  • Bake for 20 minutes.


Please note that the nutrition data is a ballpark figure. Exact data is not possible. Data is for the entire recipe. Number of cookies will vary by how large you make them. Divide this data by the number of cookies you end up with.


Serving: 1batch | Calories: 1301kcal | Carbohydrates: 132g | Protein: 31g | Fat: 76g | Saturated Fat: 30g | Sodium: 103mg | Potassium: 1350mg | Fiber: 20g | Sugar: 71g | Calcium: 574mg | Iron: 6.6mg

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  1. I made these tonight, and they were sooo good! We’ve been eating clean for about a month now, and these were the perfection solution for my sweet tooth! My youngest son, who’s 1, has milk, soy, and corn intolerances, so this was his first time trying a cookie of any sort. He loved it! Thanks for a great recipe!!


  2. What is the nutritional information? It’s not showing up when I pull up the recipe.

    Thanks and can’t wait to make these!


    1. It varies depending on how big you make your cookies. You can enter the recipe into a nutrition calculator when you know how many you have.


  3. Baked these with my 3 year old to pass a rainy afternoon today. AH-MAZING! I had some serious doubts, but holy moly!

    Did mine using a blender and everything blended up really nicely. So neat how the almonds and oatmeal combine together to make dough. I had no idea what this would look like, but it was delicous. My toddler and I were licking the bowl!

    I doubled the recipe and think 6 T of honey was too much. Will definitely cut back next time.

    My oatmeal was still warm when I added in the chocolate chips, so some of them melted and chocolate “swirl” cookies. . .so yummy.

    I cheated and used 1/2 regular choc chip with the grain sweetened. I chickened out last minute because I was afraid my toddler wouldn’t like them. Next time, I’m going to try to use the grain sweetened only.

    Great recipe! Thanks!


    1. Nikki – My pleasure! Glad you enjoyed them. 🙂


    1. Shirley – They are soft. I used the SunSpire brand chips from Whole Foods, but you can also order them online from Amazon.


  4. What can I use instead of wheat flour to make these gluten free?


    1. Brenda – You could try using almond flour or gluten free oat flour, but I haven’t tried it myself, so I’m not sure how it would turn out.


  5. Great recipe , but I would use 1/8 cup spelt flour instead of whole wheat , I stopped using modern wheat flour since I’ve read William Davis’ Book: “What Belly”…. really scary .
    Thanx for the recipe.


    1. Mey – But isn’t spelt roughly the same? I realize it’s an ancient grain, but hasn’t it been just as tampered with?


  6. do you use whole almonds or sliced almonds?


    1. Bailey – Doesn’t matter. You put everything in a food processor, so it grinds everything up anyway.


  7. Can I substitute spelt flour for the whole wheat flour?


    1. Catherine – I haven’t tried it, but I would think it should work fine.


  8. Oh these look so yummy, sadly my son is allergic to peanuts and is on a strict no nut (all nut) diet. Also, no eggs. 🙁
    Consider adding another recipe?


    1. Katrina – I can give it a shot, sure.


  9. I never seen grain chocolate chips but can I used dark chocolate.Thank for sharing!


    1. Lillie – Sure.


  10. On day 3 of clean eating and I made these tonight and they are so delicious!! But the best part is that my 4 young children liked them too… Win-Win 🙂 Thanks for all you do I would not have been able to start this journey without you and your website!!


    1. Angie – My pleasure! Mini Chef loves them too!


  11. I’m always looking for healthy dessert recipes – can’t wait to try this!


    1. Erena – Let me know how you like them!


  12. Do you think it would work to substitute carob chips for the chocolate chips?


    1. Keriann – Sure!


  13. Definitely going to try these!!! I just started my whole family on the clean eating lifestyle, and my husband and children are not thrilled. So, I think if I keep finding recipes that don’t seem so “healthy” they might jump on the bandwagon 100%, and not fight me on this. I did find the Grain Sweetened Chocolate Chips on Wal-Mart’s website, they’re in bulk, but it comes out to $5.85/10 oz. bag. That seems reasonable…doesn’t it?


    1. Laura – Wow! That’s an amazing price! I may have to check that out myself! 😀


  14. Hi!
    Can you tell me where to purchase “grain sweetened chocolate chips”??
    Thank you


    1. Paula – I used to get them at Whole Foods. But they don’t carry them any longer. However, you can still get them on Amazon, or contact the company to find out where they sell in your area.


  15. I love your site and am still very new to clean eating…Have been doing ok and eating 60-70% clean… Is there a difference between whole wheat pastry flour and regular whole wheat flour? I am a baker and want to make cookies for my home but dont want to fall off my clean eating just for a sweet tooth. Thanks!


    1. Jessica W – Here’s an article that explains the difference in flours:


  16. Would these work without the oatmeal? I like oatmeal just wodering if that makes it more like a oatmeal cho chip cookie or not…


    1. Khadijah – Not really. I mean, you could substitute something I’m sure. But I’m not sure what…


  17. I have more of a salt tooth. However when I do have the urge for something sweet I rarely have the ingredients to make anything to curb it. I live in rural Canada and sometimes do not have the access to sugar free baking ingredients if my pantry is empty. Can I substitute unsweetened bakers chocolate chopped up? Or carob chips? Thanks!


    1. Robin – Sure!


  18. Hi there! If I use almond meal would the measurement be the same? 2/3 cup?


    1. Zarah – Not quite, but I think you could get away with it. Maybe just use a scant 2/3 cup. Better to use less and slowly add more than to add too much right away.


  19. Hi there! I just tried making these and not sure where I went wrong…I didn’t use almonds and instead of pastry flour just used regular flour. From reading others comments, that should have been ok right?

    They were really dark, and very mushy, almost runny…. Any suggestions? I want to try them again tomorrow!



    1. Sarah – You can’t sub with regular flour because it doesn’t absorb as much liquid and the whole grain flour. That’s probably why they were runny. And the almonds give them some bulk.


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