AIP Chocolate Chip Cookies paleo autoimmune protocol
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After 4 months of trial and error I have finally created the world’s best AIP Chocolate Chip Cookies.

Yes, I am just going to go ahead and declare the title on this one and once you try this recipe, you are going to agree with me.

I have been testing this recipe since November and you guys have been waiting so patiently for the recipe as I shared little snippets. The wait may have been long but I truly think it was worth it!

AIP Chocolate Chip Cookies paleo autoimmune protocol

The secret or not so secret ingredient in these Paleo AIP Chocolate Chip Cookies is Sweet Potato Flour.

Sweet potato flour is not super common, and I am sorry but there is no substitute for it. This cookie is moist because of it.

The good news is that you need very little of the flour…too much of it and all you will taste is sweet potato ( I learned that the hard way). You are still going to slightly taste the sweet potato flour in this recipe but it is very mild.

The other great thing about these cookies is that they don’t require a gelatin egg.

I did add some collagen (green can) because I add it to everything (nutrient win) but no gelatin. The other ingredient that you cannot substitute is the sustainable palm shortening (coconut oil just won’t work the same). I order my palm shortening from Fully Healthy (formerly Shop AIP).

Another ingredient I wanted to talk about in these Paleo AIP Chocolate Chip Cookies is coconut flour. Different coconut flour brands behave differently in recipes. For this recipe I tried both Nutiva Coconut Flour and Bob’s Red Mill Coconut Flour.

That being said, if you are using a different brand then you may need to adjust the amount of liquid in the recipe. Here is a photo of the desired consistency you are looking for:

AIP Chocolate Chip Cookies paleo autoimmune protocol

If you need to add more liquid, add a Tbsp. of water at a time until the desired consistency is reached.

AIP Chocolate Chip Cookies paleo autoimmune protocol

I have made these cookies many many times with homemade carob chips. You can find a recipe for carob chips here.

I have also used Enjoy Life chocolate chips (which require a reintroduction of chocolate). Both are delicious and work great in this recipe! I have also made this recipe without the chips and I used cinnamon and raisins in their place instead.

There are some other cookie recipes on my blog that I know you will love…my Chocolate Tiger Nut Cookies and my Cinnamon Coconut Raisin Cookies…so first make a batch of these Paleo AIP Chocolate Chip Cookies then get your oven ready for cookies galore!

These Paleo AIP Chocolate Chip Cookies were truly a labor of love and it would really mean a lot to me if you shared this recipe with your family and friends and on social media.

Besides friends don’t let friends miss out on the world’s best chocolate chip cookie recipe now do they?!

XO Meagen Ashley

*This recipe has been shared on the AIP Paleo Recipe Roundtable

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AIP Chocolate Chip Cookies paleo autoimmune protocol
5 from 8 votes
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AIP Chocolate Chip Cookies

The best AIP chocolate chip cookie you have ever tasted!
Course Dessert, Snacks
Prep Time 15 minutes
Cook Time 7 minutes
Total Time 22 minutes
Servings 12 cookies

Ingredients

  • 2/3 cup palm shortening, melted
  • 1/4 cup honey, melted
  • 1/4 cup maple syrup
  • 1 tsp apple cider vinegar
  • 1/2 cup coconut flour, sifted
  • 1/2 cup arrowroot starch
  • 1/8 cup sweet potato flour, sifted
  • 1/8 cup Collagen Vital Proteins or Great Lakes brand
  • 1/2 tsp baking soda
  • 1/4 tsp salt
  • 1/4 cup Carob Chips or Enjoy life chocolate chips (if reintroduced)

Instructions

  1. Preheat the oven to 350 degrees and line a baking sheet with parchment paper. Mix the wet ingredients into a medium sized bowl.
  2. Mix the dry ingredients into a large sized bowl. Make a hole in the center of the bowl and pour in the wet ingredients. Stir to mix.
  3. Let the batter stand for a few minutes to thicken. If the batter is too dry, add in 1 Tbsp. of water at a time until the desired consistency is reached.
  4. Scoop a Tbsp. of the dough at a time and roll into a ball with your hands. Flatten the ball into a cookie shape on a parchment lined baking sheet.
  5. Bake in the oven for 7-10 minutes or until the edges are slightly golden brown (be careful not to overcook them).
  6. Remove from the oven and let cool for 5-10 minutes on the pan, then place on a cooling rack to cool completely.
  7. Store in the fridge in a glass dish for up to 5 days or freeze for up to 3 months.

56 Comments

  1. These look fabulous. Any replacement for the sweet potato flour, perhaps? Can’t wait to try them.

    1. Meagen Ashley says:

      The sweet potato flour is what keeps the cookies moist on the inside. You could try swapping it out with cassava flour but it won’t be the same texture then- they will likely be a bit drier.

      1. 5 stars
        Thank you for all of your hard work and sharing this fantastic recipe!

        I made my own sweet potato flour/powder by ricing cooked sweet potatoes, smearing them onto fruit leather trays and dehydrating for 4hrs @135° – I put the dried sweet potato “bark” into the Blendtec and blended until all lumps disappeared (Tip: I sealed the open blender with a loose layer of Saran Wrap before putting the lid on because the fine sweet potato powder was escaping out of the blender like smoke!).

        That being said, I also made these with cooked and smoothly riced sweet potatoes which I only partially dried (basically for 30min in the dehydrator because I was too impatient to wait 4hrs!) But drying can also be done on very low heat in the oven or even in the air fryer (mine has a dehydrator setting but the sweet potato really needs to be mashed to the bottom otherwise the fan blows it all over the place and it may burn a bit in areas before it’s all dry!).

        Another tip: I used Missy J’s carob chips which melted in the batter because the melted oil and honey were still warm so next time I let it cool completely before adding chips and they were great!

        I also added alcohol free vanilla.

        My question is about the maple syrup taste. I’d love to know if anyone has tried these to make with date syrup or maybe with a coconut sugar syrup if there is such a thing? 🍪🤎

        1. Meagen Ashley says:

          Hi there Kim,

          Thank you SO much for sharing your amazing process with everyone! You definitely put a lot of love into your batch and I’m so happy to hear that they came out successfully. 🙂

          I interchange maple syrup, honey, and date paste successfully in many recipes, so those syrup alternatives could be worth a try for sure.

          xo,
          Meagen

    2. Meagen Ashley says:

      Hi, you could substitute green banana flour or cassava flour. It just changes the texture a bit, but they will still be good!

  2. YUm!! They look delicious!

    1. Meagen Ashley says:

      Thank you! Hope you enjoy!

      1. Can we use sweet potatoes in place of sweet potato flour?
        If so, what ratio?

        1. Meagen Ashley says:

          Hi Steph,

          Please pardon my delayed reply. I hope you are well!

          Unfortunately, no that wouldn’t work. You can simply leave it out and substitute an equal amount of (preferably) cassava flour, or use more arrowroot instead.

          I hope you enjoy the cookies!

          xo,
          Meagen

        2. 5 stars
          Actually, I made them successfully with partially dried sweet potatoes – it was dried to a paste consistency – still quite moist but not wet. (If my other comment is here I explained how I did it). Maybe the sweet potato flour version is superior but mine worked out fabulously well for our liking! Actually I forgot a really important tip!!!

          Before mixing wet and dry ingredients I had to put the melted wet ingredients in the blender with the cooked and riced sweet potato because it was not fully incorporating with the other wet ingredients by hand!

  3. I’m curious what brand of sweet potato flour you use. Thank you!

    1. Meagen Ashley says:

      I ordered mine off of amazon.ca and it is the brand Paleo Planet!

  4. what brand of carob chips did you use? I have not been able to find AIP compliant ones. Thanks!!

    1. Meagen Ashley says:

      I also haven’t found any AIP compliant ones. I make my own using a recipe from flametofork.com and I bought a chocolate chip mold from amazon that I use to make them look like chocolate chips!

  5. These definitely are the best cookies!!

    1. Meagen Ashley says:

      Thank you!! 🙂

  6. I’m coconut intolerant and want to try this recipe. Any subtitution suggestions?

    1. Meagen Ashley says:

      I am not sure…you could try adding cassava or tigernut flour instead.

  7. 5 stars
    AMAZING!!!! I thought maybe it was because I hadn’t had anything other than fruit that was sweet it a long time, but my husband who won’t eat most AIP food recipes loves them. Can’t wait to try more of your recipes.

    1. Meagen Ashley says:

      Thank you so much, Faith! I love getting feedback like this! Cookies for the win!

  8. what kind of carob chips do you get? Unsweetened ones? or the regular ones?

    1. Meagen Ashley says:

      There aren’t any carob chips that are AIP as most of they have soy. So I linked in the blog post the recipe I use to make my own carob chips!

      1. Absolutely LOVED these cookies i used Missy J’s Sweet Aussie Carob Chips. Their ingredients are carob, carob powder and coconut sugar with sea salt

        1. Meagen Ashley says:

          Sounds lovely! You are very lucky to have found a compliant carbo chip!

  9. Faith McCauley says:

    5 stars
    I added some cacao to the dough I can’t wait to try them. They look beautiful

    1. You’re welcome! I hope you enjoy them!!

  10. 5 stars
    These are the best chocolate chip cookies ever! They are the closest thing to the real deal from my childhood that I’ve had since eating this way. I’ve tried lots and Meagan offers the most delicious AIP baking recipes around.

    1. Meagen Ashley says:

      Thanks so much Penny! So glad you love them- they were a labor of love!

  11. 5 stars
    I made these today…and am so glad you perservered with your recipe. They turned out terrific! Will make again. I posted a photo to Pinterest.

    1. Meagen Ashley says:

      Hi Sheryl,

      Thank you so much! I really appreciate the support. Glad you enjoyed them too!

  12. What brand palm shortening do you use? I can’t find it in Canada

    1. Meagen Ashley says:

      I order mine from naturamarket.ca I am from Canada as well!

  13. 5 stars
    Thank you for the recipe! I use this as a base for for cookies with some variation. I don’t have sweet potato flour so I tried tapioca flour instead the first time, was a crunchy but tasty cookie. The next few times I’ve used tigernut flour which makes it a more chewy cookie (yum!). Works well with dried fruit instead of/in addition to chips as well!

    1. Meagen Ashley says:

      Thank you Anu! I am so glad you like these cookies!

  14. hi! i’ve recently reintroduced eggs. how many eggs can i use for this recipe? btw I love your banana bread recipe, the one with carob chips. 🙂 thanks in advance!

    1. Meagen Ashley says:

      Hi! 1-2 eggs will work!

  15. I made a grave error. Someone help me! I mixed this all together and it was a soup even after letting it sit for a while. I alternated flours 1 tsp at a time and it still wouldn’t thicken so I put it in the fridge for a bit and it was still soupy. What did I do?!

    1. Hello Kir, So sorry to hear this was a mishap! Different flour brands can cause inconsistencies in AIP baked goods. You may wish to try adding just more coconut flour, as it is very absorbent! Try it in 2 tbsp at a time and see how the texture looks to you before baking the dough. Let me know if this helped you! – Meagen

  16. Is there anyway I can just use regular sweet potato and maybe blend it uncooked so it gets like a rice like consistency.?

    1. Hi there Tiffany, thanks for reaching out! I haven’t tried fresh, grated sweet potato as a sweet potato flour substitute. I imagine that it may create a dough that is too moist. Instead I would just add more flour – either tigernut or arrowroot or cassava should do the trick!

  17. I followed the recipe and the batter was a bit leaky even though it sat for almost 10 minutes. I still put them on the baking sheet and they all ran together into one large cookie and they were oily. They tasted well, but just don’t look very nice.

    1. Meagen Ashley says:

      Hi there Manda,

      So sorry to hear they baked up runny for you! I am going to guess that maybe there was too much coconut oil, or perhaps did you use a liquid coconut oil? You could try adding 1 to 2 Tbsp coconut flour and see if that helps bind the batter better together for you.

      xo,
      Meagen

  18. I do not know what happened as I followed recipe but they melted all over in the oven. Was a mess. Any ideas?

    1. Meagen Ashley says:

      Hi Debbie,

      I’m sorry to hear these did not turn out right for you. I am thinking that some possibilities could be the amount of palm shortening used or the brand. Also depending on climate and altitude, some baking recipes may need adapting. If this is the case, you can try either or both of these tips:

      1) Try adding a touch more flour
      2) Try refrigerating the dough for 2 hours before baking

      Let me know if you try these again and if they work out for you the next time around!

      xo,
      Meagen

  19. 5 stars
    These are great! I’m glad I was able to dip into my huge jar of sweet potato flour. I can’t seem to find many recipes that call for it! I subbed the palm shortening for beef tallow and the arrowroot for plantain flour. They are too sweet for my taste, so next time I’ll probably use a scant 1/2 cup of maple syrup and leave the honey out.

    1. Meagen Ashley says:

      Hi Rachel,

      Thank you for leaving your kind comment!

      Please let me know how they work out for you when you reduce the sweetener. You may need to increase the fat just slightly to compensate for the reduced liquid sweetener so that they are not too dry.

      xo,
      Meagen

  20. Is it possible to use coconut manna instead of palm shortening?

    1. Meagen Ashley says:

      Hi Natalie,

      Great question! Unfortunately, coconut manna won’t work as a replacement. Though you can use coconut oil instead! Just know that it will create a more dense and less “flaky” texture versus palm shortening.

      xo,
      Meagen

  21. Hi is the collagen necessary?

    1. Meagen Ashley says:

      Hi Rachael,

      Good question. 🙂

      The collagen isn’t necessary, but you may need to add some coconut flour to replace it. Try adding just 1 teaspoon at a time to see how it works for your batter, and let me know how it works out!

      xo,
      Meagen

      1. Thank you!!

        1. Meagen Ashley says:

          You are so welcome! 🙂

  22. Hi Meagen,
    Can you use squash flour instead of sweet potato flour?

    1. Meagen Ashley says:

      Hi Carol,

      I’m sorry but I haven’t tried that particular flour before, so I’m not quite sure if it would work.

      You could try to make a 1/4-size batch and see if it comes out to your liking! If you try it please let me know what you think!

      xo,
      Meagen

  23. I am not able to find the carob chip recipe or the sweet potato flour. Neither of the links off of your site work for those. Is there a way to share the carob chip recipe? I found other sweet potato flour or I may try making my own:) thank you for all your work coming up with this recipe! I’d love to give it a try if I can figure out how to make carob chips.

    1. Meagen Ashley says:

      Hello Shauna,

      Please pardon my delayed reply!

      Thank you for letting me know about those links. It appears that the sweet potato flour is no longer available from Fully Healthy, and the blogger who posted the carob chips recipe may have shut down her blog.

      Though I have not tested these chips, they may be a good substitute: https://raiasrecipes.com/2012/06/homemade-carob-chips-refined-sugar-free.html

      This sweet potato flour has great reviews: https://www.amazon.com/LiveKuna-Orange-Gluten-Free-Alternative-Coconut/dp/B0CV8K7VDF/

      I hope this helps and that you enjoy the cookies if you try them!

      xo,
      Meagen

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