Coconut Flour Pumpkin Muffins

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These Coconut Flour Pumpkin Muffins are a delicious way to celebrate pumpkin season. They are naturally grain-free and Paleo friendly, and make a great protein-packed breakfast or snack on the go!

paleo pumpkin spice muffins

Made with coconut flour, they are perfect for those who need to avoid grains and nuts,* and they are also higher in fiber and protein than a traditional muffin.

I have to admit, I feel pretty silly calling any sort of baked good “Paleo,” but sometimes it’s just the easiest way to identify a recipe as grain-free, dairy-free, and refined-sugar-free without making the recipe title so much of a mouthful. Whether you follow a Paleo diet or not, these muffins are a tasty Fall treat, great for a breakfast on-the-go or served with an afternoon tea. My son is a big fan of them, too!

(If you’d prefer a muffin recipe that doesn’t call for eggs or coconut flour, be sure to check out my recipe notes at the bottom of this post.)

Pumpkin Spice Muffins (Nut-free)

Makes 12 muffins

Adapted from these Applesauce Cupcakes


3/4 cup coconut flour
1/2 cup pumpkin puree (canned or homemade)
3/4 cup maple syrup
6 eggs
1 teaspoon ground cinnamon
1/2 teaspoon ground ginger
1/4 teaspoon ground cloves
3/4 teaspoon baking soda
1 teaspoon apple cider vinegar (or lemon juice)


Preheat the oven to 350F and line a standard muffin tin with 12 parchment or silicone baking cups. (I use these silicone cups.) In a large mixing bowl, combine all of the ingredients and stir well with a whisk to break up any clumps.

pumpkin spice muffin mix put into muffin tin

Divide the batter into the 12 baking cups, then bake at 350F for 25 to 30 minutes, until the edges are golden and the centers are firm. Allow to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.

pumpkin spice muffins with one cut in half

Store the muffins in a sealed container in the fridge for up to one week, or in the freezer for up to 6 months.

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4.45 from 47 votes

Coconut Flour Pumpkin Muffins (Gluten-Free)

Coconut Flour Pumpkin Muffins are naturally gluten-free and Paleo friendly. They make a great protein-packed treat that's bursting with pumpkin spice flavor!
Course Breakfast
Cuisine American
Keyword coconut flour pumpkin muffins
Prep Time 5 minutes
Cook Time 25 minutes
Total Time 30 minutes
Servings 12
Calories 121kcal



  • Preheat the oven to 350F and line a standard muffin tin with 12 parchment or silicone baking cups. (I use these silicone cups.) In a large mixing bowl, combine all of the ingredients and stir well with a whisk to break up any clumps.
  • Divide the batter into the 12 baking cups, then bake at 350F for 25 to 30 minutes, until the edges are golden and the centers are firm. Allow to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.
  • Store the muffins in a sealed container in the fridge for up to one week, or in the freezer for up to 6 months.


Calories: 121kcal | Carbohydrates: 18g | Protein: 3g | Fat: 3g | Saturated Fat: 1g | Cholesterol: 81mg | Sodium: 117mg | Potassium: 96mg | Fiber: 3g | Sugar: 13g | Vitamin A: 1705IU | Vitamin C: 0.4mg | Calcium: 39mg | Iron: 0.8mg


The American College of Allergy, Asthma & Immunology (ACAAI) states: “Coconut is not a botanical nut; it is classified as a fruit, even though the Food and Drug Administration recognizes coconut as a tree nut. While allergic reactions to coconut have been documented, most people who are allergic to tree nuts can safely eat coconut. If you are allergic to tree nuts, talk to your allergist before adding coconut to your diet.”

If you try these Coconut Flour Pumpkin Muffins, please leave a comment below letting me know how you like them. And if you make any modifications, I’d love to hear about those, too! We can all benefit from your experience.

Reader Feedback: What’s your favorite way to enjoy pumpkin?

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I was wondering if this recipe would work as donuts like the banana donut recipe worked for muffins?

Danielle @ Chits and Chats and Chocolate

Being mostly grain free, a good muffin recipe is hard to come by, but these look fabulous! My favourite way to enjoy pumpkin is probably the traditional pumpkin pie.


I just love pumpkin seeds. I use them in salads, trail mixes and just plain snacking.

But just yesterday, I was craving that Fall pumpkin feeling and unfortunately downed 2 pieces of pumpkin pie in one sitting. Really wishing I had made these delectable looking muffins instead. You live and learn. Pumpkin flavoring anything is the best!


Can some of the maple syrup be substituted with coconut oil or apple sauce?


    I tried replacing 1/4 cup of the maple syrup with more pumpkin puree, and the resulting texture wasn’t as good. If you don’t mind the muffin texture being heavier/spongier, then feel free to make the adjustment.


      I used 2 tbsp of maple syrup, 1/4 cup applesauce and 3 droppers of vanilla cream stevia and added more cinnamon & pumpkin pie spice. Tasted good but the texture was off, so hard to bake with stevia, but I can’t tolerate much sugar.


    I used 1/4 cup raw honey and 1tsp. of vanilla. I didn’t taste the original, but I think they turned out well. Rather moist.


I cannot wait to make these. I have been wanting to make a pumpkin muffin, but am trying to limit grains. This looks perfect. I have loved everything I have tried from your website. The almond butter pancakes are a new weekend tradition. The chickpea “egg salad” is amazing. We are having the spaghetti squash casserole tonight. Thanks so much for all you do!

Emily @ Glitz Glam Gluten-Free

Ohh these look absolutely delicious!! I love pumpkin in baked goods and just had a pumpkin muffin yesterday!


These look amazing! Can this recipe be adapted to a loaf pan? How would I need to change it?


    I think it would work well as a loaf, too, but I’m not sure how long you would need to bake it. Probably longer, and maybe lower the temperature slightly so you don’t burn the edges before the center is baked through. Please let us know if it works for you!


      I tried baking this in a loaf pan and it turned out wonderfully! Normally I find coconut flour to be too “gritty” for me, so I tried something new. I sifted the measured coconut flour. Then, with a whisk I beat all the ingredients EXCEPT the baking soda until it looked really smooth.Then I added the baking soda. I used a standard loaf pan and baked at 350 for 30 minutes, checked it, 10 more minutes, checked it, and finally 5 minutes. It is wonderful! The texture and flavor is spot on. Definitely making this again, thank you!

Michele @ Two Raspberries

these look deliciously moist and yummy! i love that they are GF and nut free 😉


like everything else you come up with, these look delicious and simple to make! I’m curious about the maple syrup substitution as well- is it more for consistency or sweetness? could it be substituted with stevia/coconut sugar or apple sauce or coconut oil like Monica’s suggestion?


    This amount of maple syrup created the texture and sweetness I was going for– these muffins taste more like a mainstream pumpkin muffin. I did try a version that replaced 1/4 cup of the syrup with pumpkin puree, and the resulting muffin was less sweet and pretty dense. My mom didn’t like them, but I didn’t mind them… so experiment at your own risk! Just make sure you use enough moisture, too. Coconut flour needs a LOT of moisture to come out well, so dry ingredients like stevia and coconut sugar would require adding oil or extra eggs to compensate.


You seriously have the best recipes. I love using your holiday/seasonal recipes as everyone loves your recipes! Thank you so much <3


Is there an egg substitute that would work? I normally use applesauce. Would that work in these?


    No, egg substitutes don’t work well with coconut flour. Check out the link to the vegan recipe I posted above!


I just made my first batch and they taste delicious! I wish I had used a whisk to make sure everything was thoroughly blended though, even though I thought I had done a good job mixing. There were a few bites that tasted more egg-y than others. Other than that, is a wonderful, gluten-free recipe that I will make again! Thank you!!


I checked the Amazon page for the silicone cupcake molds you use and they are made in China. Many have said heating silicone is not safe and anything from China is questionable. What research did you do to determine purchasing this particular brand?


    I was actually gifted this set when I was working on my cookbook, but I’m disappointed to hear that they are made in China! I actually don’t see anything about that on the Amazon page, but perhaps it’s because I’m on a mobile device instead of my laptop. I’ll let you know if I find a better alternative– I try to only share products I’ve tried myself, and these particular cups work so well!

Kezia @ Super Naturally Healthy

Perfect just been trying to make some red velvet cupcake with coconut flour and after reading your recipe I think i was using far too much vegetable in my recipe will try out your ratio and hope for the best – coconut flour is a tricky customer sometimes!

Ceara @ Ceara's Kitchen

These muffins look wonderful and like a perfect fit for my first whirl into the world of coconut flour! Pinned!


Can you use something else besides coconut flour? My child is allergic to coconut.


Hi! These muffins look fab! Can I substitute regular flour for the coconut flour? Thanks!


So excited it’s pumpkin season! These are on my to-make list for sure. Also added them to a roundup of fit finds this week too 🙂


Do you think I could replace the coconut flour with spelt flour?


    No, I would never try replacing coconut flour in a recipe– it’s just way too unique from other flours. Perhaps try using the spelt flour in the vegan pumpkin recipe I linked to in the post above?


Love, love, love these! I made them for a family picnic this past weekend and everybody loved them. My sister, who said she usually doesn’t care for some of the recipes I make for my Primal lifestyle, loved them! I added some chopped walnuts and used a low-carb cream cheese icing I have and sprinkled them with a few more finely chopped nuts. They look beautiful and taste amazing! Perfect for that first fall dessert and I have a feeling they will make an appearance several times again this year.

Thank you so much for all of your recipes. They have seriously changed my life. I appreciate your time and effort and especially your creativity and devotion to a healthier lifestyle.


These are fabulous! I sprinkled chopped pecans on the top before putting them in the oven and patted them down! Extra yummy!


I just tried these, but with persimmon puree instead of pumpkin since I was out of pumpkin and had the persimmon on hand. They were wonderful! I did two batches – one as listed and the other with flax eggs instead of eggs. I know it’s suggested not to use egg substitute, but we thought they came out great either way. We tried them side by side and the only difference was the look of the muffins and the texture. The flax ones didn’t have the pretty rounded top and were a bit denser, but not super heavy. The taste was almost identical on both. My son(5) actually prefers the flax ones to the egg ones.

Nono Osuji

Is coconut flour gfree?


Have you ever baked with quinoa flour? Would that possibly work in this recipe? Can’t wait to try this!!


I just made these they are so good! I made a double batch and did 6 eggs and 6 egg white substitute. They turned out well! Thanks for the recipe!

Athletic Avocado

These look so perfect for fall! I was looking for ways to use up my coconut flour! This recipes looks perfect! Thanks for sharing! 🙂

April East

Exactly the texture and flavor I was looking to get!IThey were really good.I added some blueberries I had froze this summer.

Tami Adams

Do you have the nutritional information on these? Specifically the carbs? I have a T1 diabetic and we have just started paleo and I’m surprised that most recipes don’t offer this information. I can add it up myself but its nice when its included.

BTW just made these and they are fantastic! Thanks!

Genelle Pretty

These are so good! I just made a batch and ate two. Thanks for an awesome recipe! 🙂


This looks so good. I don’t have all those individual spices- except cinammon-can I sub them out for pumpkin pie spice and then add cinnamon? How much p.pie spice? Thanks!


Made them tonight they are my favorite yet 🙂


Made these this morning- AMAZING flavor and texture and kept me full for hours when paired with some coconut yogurt.

I realized after I started making them that I only had 5 eggs. While the muffins tasted great, they stuck to the paper liners pretty badly. Don’t know if this is because I didn’t have enough egg.


These look great! Can’t wait to try them. Do you think I could substitute the maple syrup with the same amount of honey?


Hi Megan, I love your recipes. You know how to make healthier treats taste so good! I’m making these muffins later…do you think I could add dark choc chips to this? Or do you think pumpkin and dark dark chocolate don’t go together? If so, would it alter anything else in the recipe?


    I think dark chocolate chips would be a great addition! I don’t think you’d need to change anything to add those. Hope you enjoy them!


I subbed 1/4 or the maple syrup for a small smashed banana and about a tsp coconut oil and a TBS almond milk. I also mixed in dark chocolate chips/craisins/pumpkin seeds. They are amazing!!


I made these this morning, and love them! I ran out of maple syrup, so I did 1/2 cup maple syrup and subbed 1/4 cup of water to keep the consistency. They were plenty sweet for me, and the texture was great! Thank you for sharing


DELICIOUS!!! (as are all your recipes!)

myndi orr

Just had these and I was surprised they didn’t taste eggy…They were great!


I have a few questions:

1. Has anyone tried using banana as an egg substitute for this recipe?
2. What are the effects of adding a dairy free milk?
3. Can sugar and dairy free butter be successfully used in place of maple syrup? If so what would be the measurements?


These are amazing! I am newly Paleo and can’t get over how great these taste. The texture is wonderful. My whole family loved them-including the picky eater 🙂


Hi I was wondering if it’s possible to substitute something else for the apple cider vinegar/lemon juice (can you omit it?)

Deneen M

can I use sugar free maple syrup? I’m diabetic, but would love to make these as I also follow a paleo diet. thank you.


these are great! we recently just started paleo and so far it has been wonderful! I ended up making 2 loaves from this recipe (by doubling it) I was wondering what is the best way to store these and how long will it stay fresh?

TIA! 🙂

Don Warga

how many net carbs per muffin?


I have used this recipe many times and it is now my go-to. My kids love these and so did friends!


What flour could you sub out for the buckwheat in the vegan, my son is gluten free, soy free casien free.


    Megan Gilmore

    Buckwheat is already gluten-free– despite its confusing name, it isn’t related to wheat at all!

Jeanne Shepherd

My daughter is allergic to buckwheat, coconut and almonds and eggs. Any ideas on how to make these muffins without the above ingredients? Thank you!


    I would try using a combination of rice flours and substituting for a flax or chia egg!

Carmen meli

Is there a substitute for coconut flour, please? Like for example using plain flour and shredded coconut? The reason being that I don’t find coconut flour here in France and I really love coconut!

Maureen fleet

Help! I’m totally panicked! I have always enjoyed your muffins but recently I have discovered food sensitivities to eggs and almonds! What is a healthy muffin lover to do???


Do these taste eggy? Since going gluten free, I’ve tried a lot of paleo recipes, but I don’t like the eggy flavor that a lot of the paleo recipes leave in my mouth. Are there any egg substitutes that work and don’t taste eggy?

    Megan Gilmore

    I know what you mean, and in this particular recipe I don’t think you can taste the egg at all.

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