AIP Pumpkin Muffins

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These pumpkin muffins come courtesy of our friend Mary Lapp, an original member of the AIP blogging community. When she decided to transition her website to focus on new endeavors, she wanted to know if we’d be happy hosting some of her classic recipes, and of course we said yes!

This is a fantastic base recipe that makes lovely muffins or even a cake. What I love about Mary’s recipes is that she gives lots of instructions and options for substitutions. I’ve edited this recipe to reflect my favorite combination, but you can see her suggestions in the “notes” section at the bottom of the page.

4.6 from 12 reviews
AIP Pumpkin Muffins
Prep time
Cook time
Total time
Serves: 12 muffins
  1. Preheat oven to 350 degrees F and prepare a muffin tin.
  2. Add the water and applesauce to the bottom of a small saucepan and stir to combine. Sprinkle with the gelatin, and set aside to "bloom" for a few minutes.
  3. Meanwhile, combine the cassava flour, coconut sugar, arrowroot, baking soda, cinnamon, and salt in a large bowl and stir to combine. In a medium-sized bowl, combine the pumpkin and avocado oil, using a whisk to combine.
  4. When the gelatin has been absorbed by the liquid, turn the heat on the lowest setting and continuously whisk to combine as the mixture gently heats up. When the gelatin has completely dissolved (slightly warmer than room temperature), turn off the heat and combine with the pumpkin mixture before combining all of the wet and dry ingredients together. Your batter will be a touch drier than traditional cake or muffin batter; this is normal.
  5. Use a spoon to fill 9-12 muffin cups with batter. Bake for 20-25 minutes, or until a toothpick comes out clean.
  6. When they are finished cooking, cool for 10 minutes in the pan before transferring to a wire rack. Allow to fully cool to develop the right texture.
Flour Substitution Options:

1/2 cup tigernut flour, ½ cup cassava flour, ½ cup arrowroot flour
1½ cups cassava flour
1 cup cassava flour, ½ cup tigernut flour


About Mickey Trescott

Mickey Trescott is a co-founder here at Autoimmune Wellness and a co-teacher of AIP Certified Coach. After recovering from her own struggle with both Celiac and Hashimoto’s disease, adrenal fatigue, and multiple vitamin deficiencies, Mickey started to write about her experience to share with others and help them realize they are not alone in their struggles. She has a Master's degree in Human Nutrition and Functional Nutrition, and is the author of three best-selling books--The Autoimmune Paleo Cookbook, The Autoimmune Wellness Handbook, and The Nutrient-Dense Kitchen. You can watch her AIP cooking demos by following her on Instagram.


  • Megan says

    Does it really call for a full cup of coconut sugar? It just sounded like a lot of sugar. Thanks!

    • Mickey Trescott says

      Yes, and it makes 12 muffins or a small cake!

  • Mitzi Marquez says

    Can coconut or almond flour be used as a substitute?

    • Mickey Trescott says

      Mitzi, I doubt coconut flour would work (the texture is very different) but almond might work – I haven’t tried it personally though. Let us know if you discover anything food!

  • Heather says

    So is this recipe safe for the 1st phase of the diet? Sounds delish!! I am fairly new at this. It calls for coconut sugar, and I thought honey and maple syrup were the only 2 sweeteners allowed. Are all the recipes on this site supposed to be for the 1st, most restricted phase? Thanks!

    • Angie Alt says

      We saw you asked this question in another spot too. Yes, coconut sugar is compliant. Yes all the recipes on the site are elimination phase compliant. AIP is not a no-sugar protocol, but it is a low-sugar protocol & we try to focus on sweeteners that have some nutritive qualities. Thanks for being here!

      • Heather says

        Thanks for the timely response! I was having some internet issues and didn’t think my first comment went through, so I posted it again when I was reading on your site. Sorry about that! 🙂 There is so much information here, and I am so thankful to have access to it! I am definitely going to make these muffins soon! THANK YOU for the recipes, all the helpful info, and sharing your stories! I have a lot to learn, but I’ll get there!

    • Mickey Trescott says

      Hi Heather! Everything we post here is elimination-phase compliant. Honey, maple, and coconut sugar are all allowed in moderation.

  • Susan A Inks says

    Can the avocado oil be substituted with coconut oil? Thanks, Sue

    • Mickey Trescott says

      Susan, I would start by trying a mild-flavored olive oil, but coconut oil may work too.

  • Kimberly says

    The recipe calls for 1 cup cassava flour but the substitute options say 1 1/2 cups. Is the extra 1/2 a cup to replace the gelatin?
    Thanks. I am excited to try this out.

    • Mickey Trescott says

      That version would be 1 1/2 cups to replace the 1/2 cup arrowroot flour! Hope it helps.

  • Sherrie says

    Hi there,
    I’m seeing gelatin used in a lot of baking recipes and am curious what its purpose is or what it does in baked goods. I would love to try these but don’t have gelatin. Is there a substitution? Thanks!

    • Angie Alt says

      The gelatin replaces egg in a lot of AIP baking. Other substitutes will probably change the texture of these.

  • mom2one says

    Hi Angie and Mickey, what do you know about oxalates? I had a Organic Acid Test done and it came back with high levels of oxalates. I’ve since had to go on a low oxalate diet and have found that the foods that were once staples in my AIP/Paleo diet (i.e. cassava flour, arrowroot powder, cinnamon, spinach, sweet potatoes, etc.) were very high in oxalates. I’ve noticed lot of my symptoms improving since cutting out a lot of these high oxalate foods. I just wondered if there isn’t more of a connection with oxalates and autoimmune symptoms.

    • Mickey Trescott says

      Hi! I have done some exploring about oxalates, but personally, and in my work with clients, I have found their potential to cause issues overblown. A lot of the foods you mention are also high in starch, which I do know many folks can react to because of dysbiosis. Personally I would rule out gut issues working with a skilled practitioner versus cutting out a lot of vegetables that also happen to be quite nutrient-dense. An exception would be folks who suffer from kidney stones they know are caused by oxalates. Dr. Ballantyne has a great article here you may find informative:
      Hope it helps!

  • Babz says

    I made these muffins yesterday and couldn’t wait to eat one, so I ate it before it cooled completely. It tasted great, but the texture was a little mushy near the bottom. After I let them cool completely I froze them and thawed a couple in the microwave this morning for about 40 seconds (on high). And you are absolutely right – the texture improved by letting them cool completely – they were absolutely perfect!

    • Mickey Trescott says

      Babz – that is a funny thing about AIP baking – cooling is almost as important as cooking! Good to hear they turned out for you!

    • Marybeth says

      So 1 cup of coconut sugar is permissible!? It seems excessive
      I was under the impression sugar of any type should be minimum for a healthy diet.

      • Mickey Trescott says

        Hey Marybeth! Yes, AIP is not a sugar-free protocol. At 12 muffins, 1 cup sugar ends up being a little more than a tablespoon each. Some people choose to avoid sugar all together, but others like to have a treat now and then. This recipe fits that bill perfectly 😉

  • Laura G. says

    I really needed to have a treat that I could tolerate and saw the recipe for these muffins. I wasn’t sure if they would come out the way they looked, but they did. I enjoy the taste and are perfect when I just need something to satisfy my craving. I will definitely be making these again! Thank you.

  • Jenny Klug says

    I made these. The first batch I took out of the pan before the 10 minutes. The second batch I left them in. There was a difference in the texture to be sure. Letting them cool is key. They taste wonderful, you just have to expect them to be a little “spongy”. I will be making these on a regular basis. Thanks for the recipe.

    • Mickey Trescott says

      Thanks for sharing the results of your experiment Jenny! I agree, cooling is a whole part of the process with AIP desserts and necessary for the right texture.

  • Lisa Rose says

    can we use agar instead of gelatin?

    • Mickey Trescott says

      Hi Lisa, I’ve never used agar, but you are welcome to experiment!

  • Karen Hanna says

    Hi! Is it possible to leave out the coconut sugar or substitute it with honey or maple syrup?

    • Mickey Trescott says

      Hi Karen! No, you can’t substitute solid sugar for liquid sugar in baking recipes. While all sugars don’t behave the same, if you are looking to run your own experiment and try a swap, you should try something like maple sugar or date sugar instead of the coconut sugar.

  • Paige says

    These were so great! I rarely attempt sweet treats anymore, but even the husband approved. I loved the flavor and texture. I froze half and they reheated well.

  • Erin says

    I didn’t find arrowroot powder in any stores yesterday. Is there anything else I could use instead?

    • Mickey Trescott says

      Hi Erin! I haven’t tried this, but sometimes tapioca starch will sub well for arrowroot.

  • Laura says

    Hi – I’m allergic to coconut so I’m having a tough time finding recipes I can make….or much of anything to eat! Can the coconut sugar in this be substituted with something else?

    • Mickey Trescott says

      Hi Laura! I haven’t tried it before so you’d need to do your own experiment, but I think date sugar may work OK for this recipe. Hope it helps!

  • Brooke Beauchamp says

    I clearly messed something up cuz these were VERY gummy. I didn’t have cassava flour so I used tapioca..
    Maybe it was too fine? The flavor was good but eating a gummy bear muffin was a little off putting for sure.

    • Mickey Trescott says

      Hi Brooke! Tapioca and cassava flour are not interchangeable! Bummer!

  • Melissa says

    Starting AIP this week and made these for breakfast. They’re DELICIOUS! And thanks for the tip about cooling – the bottoms were a little gummy at first but I definitely didn’t let them cool completely. I just had to try one 😊

    • Mickey Trescott says

      Melissa, I’m glad you enjoyed them! And I’ve found that AIP baking recipes are super finicky about cooling. It is an important step in developing the right texture!

  • Amanda says

    I followed recipe exactly and the outside got hard the middle was mushy. Didn’t bake and I left it in longer than 30 minutes.

    • Mickey Trescott says

      Hi Amanada, did you let the muffins cool completely?

  • Rachelle says

    This is my 3rd try at baking AIP muffins. Two other attempts from other providers but all using same AIP ingredients basically. These, as others, turned out gooey in centre or bottom. Do you know which ingredients would cause this? They taste great but need to find solution for texture. Thanks 😊

    • Mickey Trescott says

      Hi Rachelle, are you sure your oven is cooking at the correct temperature, and what kind of muffin tin are you using?

  • Can you make this in a bread pan to make pumpkin bread instead of muffins?

    • Mickey Trescott says

      Gretchen, I haven’t done this before, so if you try it out, you’ll be running your own experiment! I think it might work with a longer cooking time.

  • Rosie Marcelo says

    Which brands of coconut sugar do you recommend

    • Mickey Trescott says

      Hi Rosie, I have used Wholesome and Nutiva in the past!

  • Holly says

    These are SO GOOD!! AIP baked goods can be kinda weird sometimes but these were so perfect you wouldn’t know they were AIP. Given all the recommendations to wait until they were completely cool I actually did and the texture was light and spongy. My husband and I ate the first batch in 2 days and he’s already wanting more – this is definitely going into our rotation!

    • Mickey Trescott says

      I’m so happy you loved them Holly!

  • Clara says

    These are so good. They are so good, I have made them there times and I’m only on week two of AIP. I have transitioned from 12 years of being 100% plant based, to paleo/ keto for 9 mo, and now trying AIP. After the birth of my first daughter I was diagnosed with many food allergies including most nuts, gluten, and landed myself with an inflammatory disease, Rosacea. Trying to heal the gut I have found myself here. It took me a long time to get the nerve to eat meat again but I have found your your website, cookbook, and podcasts extremely helpful and enjoyable to do so. Loving these backed goods like this so not only can I have a yummy treat, but also serve them to my 100% plant based husband (i skipped the gelatin and just used coconut milk fat) and my dairy free kids. Thanks!

    • Mickey Trescott says

      Welcome, Clara! Happy this recipe was a hit for you!

  • Kalie says

    These sound awesome, but I can’t do anything with apples. Can I sub the applesauce for something else, or maybe omit entirely? Would love to hear your thoughts! Thank you!

    • Mickey Trescott says

      Hi Kalie! I haven’t tried this, but you could try banana instead of the applesauce!

  • Kalie says

    Will do! Thanks!

  • Jessica says

    I’m obsessed with these! They’re SO good! curious if you know the macros per muffin? I may try to do the math.

    • Angie Alt says

      Hi Jessica, sorry we don’t provide the macros. Glad you love them!

    • Mickey Trescott says

      Hi Jessica! We don’t provide nutritional info, but it should only take a minute or two to plug into a calculator to find out.

      • Kat says

        Can you suggest possible calculator websites to find out the nutritional info?
        Can’t wait to make these. Thanks

  • Marisa says

    Just curious if you can leave the applesauce out altogether.

    • Mickey Trescott says

      Hi Marisa, no I don’t recommend leaving out any ingredients, or the recipe is likely to not turn out.

  • Kasie says

    So thankful I saw this recipe at just the right time! I was feeling so defeated at 6 days in not being able to feel satiated from just meat and veggies. This was such a nice afternoon treat to help fuel me and make me feel better about continuing on with the elimination phase. I think I undercooked them a little, but the flavor was wonderful! I omitted the coconut sugar and used a little honey to sweeten instead since I am also eliminating coconut as a potential trigger. Will be eating these whenever I feel that “I can’t do this” feeling! 🙂

  • Elizabeth says

    These came out so good! Cooking is key let me repeat cooking is key 🙂

    • Elizabeth says

      That should say cooling! Cooking is also key lol but I was trying to say cooling! My phone had other ideas

  • Mindy says

    How many eggs does the applesauce/water/gelatin mixture replace? I am thinking 4 eggs?

    • Mickey Trescott says

      Mindy, I am not sure specifically as many AIP recipe authors don’t adapt non-AIP recipes, they start from scratch. If you try adding eggs to this recipe, you’ll be experimenting on your own!

  • Sara says

    I love this recipe so much! Just started AIP about two months ago. Before that, I did a lot of gf/df/ef baking, but this was my first recipe using a gelatin egg. I love the texture so much!! This recipe isn’t overtly pumpkin, so I use this as a base for all my muffins and add in whatever I have to make different flavors (apple chunks, strawberry chunks, homemade swirls of AIP jam, etc.) I never want to lose this recipe!

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