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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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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Made these today and they are gone. Kid tested mother approved!


When a recipe is baked with eggs is that proper food combining? My guess is not unless you use a flax egg or chia egg but then can those be mixed with flour?
Im trying to figure out how to make properly combined recipe when baking. Hope you have some good tips?
I love this blog!!!


I just made this recipe using 1/4 cup of plain, organic applesauce in place of some of the maple syrup as I don’t like overly sweet muffins, and they came out fabulous tasting! they’re a big spongier than I expected, but I don’t mind.


These were seriously incredible! My whole family, including my 2 year old devoured the whole dozen in 2 days. I will be making more today. Thanks so much for sharing.


We don’t eat real sugar (of any kind, maple, agave, or otherwise) if we can help it – trying to control an autoimmune disease.

Do you think these would work if I left it out? I’m worried about the texture since maple syrup is a wet ingredient. Could I sub coconut milk? The one thing I can eat sparingly is Stevia, although we try not to overdo it.


Is it possible to sub flax eggs? Egg replacer? I have this same question for your banana blender pancakes in your cookbook.

    Megan Gilmore

    Flax eggs are usually a disaster with Paleo baked goods. Maybe the egg replacer would work, but they’ll probably be really flat– the eggs are what give it structure. I haven’t figured out an egg substitute for the pancakes, either, but I’ll be sure to post an update if I figure it out.


Smelled amazing when cooking but ended up tasting pretty bland to me. Might be because I’m new to paleo and used to the insanely sweet ones.

    Alexa W.

    I thought the exact same thing! I put a little bit of Betsy’s Best Peanut butter on top and they were great! Gave it the extra taste they needed.


Chia seeds are great egg replacer. I made very good buckwheat pancakes with them.


Anything that can be used instead of coconut flour (I’m allergic- oddly enough the doc refers to it as a nut allergy) ?

Thank you!!!

    Megan Gilmore

    I’m working on a vegan version that doesn’t use almond or coconut flour– hopefully it will be ready to post soon!


just made for my diabetic daughter , made them mini muffins only 8 carbs per muffin she is to say the least ecstatic, thx so much they are delish


Can you use less eggs? I made it and it was great, just tasted a little too much like egg though.

Jill Sandmeier

Just getting into a healthier way of eating, and trying to do no gluten, soy, dairy, sugar, corn, or caffeine. I read somewhere that too much maple syrup for sweetening can hinder weight loss goals, so I’m wondering if you could use half applesauce, half maple syrup.


    Jill, this sounds like a great idea! I’m not sure the best ratio of the two ingredients, but it would definitely be a worthwhile experiment! Did you end up trying this and if so, how did it turn out? 🙂

      Mary Patricia Fratesi

      Coconut flour swells significantly when mixed with the wet ingredients. At first seems out of proportion however quickly swells and looks as a normal batter.


    HI Jill,

    I made the recipe with 1/2 cup applesauce and 1/4 cup maple syrup, and they turned out great!


I made these for the second time today, I’m obsessed! This time I added dried cranberries and chopped pecans and it took them to a whole new level. Thanks for sharing the recipe!


I thought these were great! I am not a big ginger fan so left out the ginger and cloves and still so yummy. My 2 year old loved them as did my husband who doesn’t like coconut. I did cook a bit longer until they were pretty brown. I cannot wait to try more coconut flour recipes now.


Really yummy!! Thanks for the great recipe. I used a sweet potato, as pumpkin is not easy to find where I live… and added chocolate chips to entice my six-year-old to eat a healthy breakfast. We have been making your raspberry muffins and almond pancakes for years. I haven’t found another site with such simple healthy recipes. You have really helped us change our lifestyle. 🙂

AJ Young

So good! Thanks for an awesome recipe.


Really good. Not eggy like some we’ve tried. Just made these for my 2 year old and she’s back for seconds. Perfect size for her hands and great way to sneak in some things she might not eat otherwise. Thanks for posting!

Donald Morgan

What is the carb count. I am in ketosis and intend to stay there.


I left out the cloves and added cardamom. Delicious! My kids ate them all. Not eggy like other recipes I’ve tried.
I wonder if I could make a banana version by subbing it in for the pumpkin? Any ideas?

    Denise denis

    Yes- just subbed banana for pumpkin because I didn’t have any pumpkin and they are Great!!!
    I have made this pumpkin recipe 175 times. I love these muffins!!

Tami Rupe

I am allergic to all forms of nuts. When you say they are ‘nut free’ and have coconut flour, that makes no sense. Coconut is a NUT. Therefore, I will substitute a gluten free flour.

It is difficult to do Paleo when you are allergic to nuts and Diabetic!

Thanks for the recipe!

    Megan Gilmore

    The American College of Allergy, Asthma & Immunology classifies coconut as a fruit, not a botanical nut, and has stated that most people who are allergic to tree nuts can safely eat coconut, which is why most recipes will be labeled “nut free” even if coconut is included. If you are allergic to tree nuts, it is definitely recommended that you talk to your allergist before adding coconut to your diet, though!

    Shelia Senghas

    After 25 years as a diabetic, healthy Paleo eating cured my diabetes in 8 months..


Thank you for posting, I like alot of what you share, but these didnt taste well.
I wonder if the type of coconut flour makes a difference, as I changed brands.
Tasted baking soda, over sweet, sponge like.
I really wonder if the coconut brand makes a difference.

    Sue Wheeler

    I made them today and mine don’t task good either. I used organic coconut flour, I used Libby’s 100% canned pumpkin mane am wondering if that’s what I did wrong.


I made these this morning. I make my own pumpkin puree and freeze it in 2 cup packages. So, I took this recipe and quadrupled everything except the eggs. I only had 16 so that is all I used. Also, instead of quadrupling the maple syrup, I used half maple syrup and 1/2 raw honey. It took a little longer baking time but they turned out absolutely delicious! The texture was just like pumpkin bread and with a little bit of whipped topping on top made it taste just like pumpkin cake! I took these to a potluck and they were gone. Quick and easy to make too.


The first time I made these they were really grainy. The second time I doubled the pumpkin and they’re much better now. The flavor of these muffins is great! These are going to get made a lot because they’re the easiest, yummiest paleo muffins I’ve found!


What are the nutrition facts for this recipe? Watching my carb intake, so just curious. Thanks!


I’m also curious about the nutrition facts. Do you have them available by any chance?

    Megan Gilmore

    I don’t, but you can use a free nutrition calculator like to quickly calculate what you need!


Is there a way to cut down the sugar (maple syrup?)


Well, I can’t say I’ll make these again. We’re pretty disappointed about how these muffins turned out, and I’m not sure what the issue was. I used organic coconut flour and canned pumpkin, and the muffins were eggy and not smooth on the tops (or as smooth as your pics are showing). I’m a bit surprised that the recipe calls for so many eggs and so much maple syrup. We doubled the recipe (a mistake for making a first-time recipe), and we “wasted” a dozen eggs and a bottle of syrup.


Now that the fall season is here I wanted a Paleo pumpkin muffin recipe. I found it here. These muffins were delicious. Goodbye Dunkin Donuts pumpkin muffins, hello Paleo (healthy) pumpkin muffins!!!


These were amazing! Usually pumpkin muffins with coconut flour taste more like flan (super eggy). These tasted like really moist muffins. I had to use only 1/2 cup of maple syrup because I ran out, so I subbed in an extra 1/4 cup of pumpkin puree, 4 drops of stevia, three packets of xylitol, an extra splash of ACV and they turned out delicious and moist. Thanks for a great recipe. My favorite pumpkin recipe is usually pumpkin pie, but these are my new favorite pumpkin treat.
PS- to those who say they came out too sweet, make sure that you aren’t using pumpkin pie filling. There is a huge difference between canned pumpkin and pumpkin pie filling (and they are usually stocked next to each other in the grocery store).


These are fantastic! I’m going to make another batch this week. My four-year-old is eating them too fast!!!! Thank you! Thank you!


Has anyone tried adding ground flax? Thinking of adding 2 tbsp of ground flax to amp up the protein and fiber in the muffins 🙂


These are really good! My 10 year old loved them and she’s pretty anti-low carb, lol.

Today I made my second batch and I made these adjustments:

1. I used sugar free syrup. I’m type 2 diabetic, so the lower the carb content,the healthier my blood sugar will stay.
2. Added 1/4 a cup of Stevia. I found my first batch lacked sweetness. Could be because I decided to use sugar free maple syrup perhaps?
3. I sprayed Pam into the parchment muffin cups in butter flavor. I noticed that with my first batch, they stuck really bad on the parchment paper and I lost about 1/4 of the cupcakes to the paper.


For those wondering about nutrition, I put the ingredients in MyFitnessPal (obviously actual nutrition may vary a little depending on brands), but if you make 12 muffins each muffin is roughly 120 calories, 4.2g protein, 3.6g fat, 31g carbohydrates, 3g fiber, 28g net carbs, and 26.8g sugar.


Pretty tasty! I doubled it so used an entire can of pumpkin puree, 1.5 Tbsp pumpkin pie spice (instead of the pumpkin pie mix), 1 Tbsp vanilla extra and for the sweet ended up using 3/4 cup maple syrup + 1/2 cup honey (for a double batch). Doesn’t have that coconut flour aftertaste baked goods can sometimes get. Yield was 24 good sized muffins we’ll eat throughout the week for breakfast and freeze the extras. Recommend.


I tried these too I subsituted applesauce for 1/2 maple syrup and added chocolate chips and pecans I liked them but they didn’t look nothing like your picture the coconut flour absorbed all the liquid so next time I’m using almond flour and coconut flour


Can you make these with flax eggs? If so how many?


These muffins were just way, way too sweet for me and my family. Each muffin has 13 grams of sugar from the maple syrup alone.

    Megan Gilmore

    You’re welcome to tweak it to suit your tastes! I always aim to please people coming off of refined sugar treats to help them gradually transition without feeling deprived, but if you’re already avoiding that stuff, you won’t need it as sweet.


My family loves these muffins, thank you and they taste delicious!! We are doing the Whole 30 as a family and has caused many tears from my 10 year old during school birthdays and when other treats are passed around. We decided to allow “paleo muffins” for these days at school and occasional breakfasts (kids can only do eggs for so long lol!). What a hit! Even my picky “nearly teenage” 12 year old loves them! Also what I love is how stinking easy they are to make! I am grateful to have found this awesome recipe and will be a keeper long after our Whole30 journey is over:)


So I made these by substituting maple syrup with unsweetened apple sauce- and they were amazing! Def will be a fall staple in my home!

Karin Krafcisin

These look so delicious but I can’t eat eggs 🙁 I see that eggs are in so many Paleo recipes too. I know I can replace eggs with flaxseed and water but when there are six eggs to the recipe, what do you do? Thanks in advance for any suggestions. I’m also intolerant to almonds and bananas which is another bummer- lol.

Dana Al-Sheikh

Hi! So this one tasted quite metallic. I think maybe baking soda is too much. Can i reduce the quantity? If so, by how much?


This recipe is great! I added 2 tbsp of flax seed meal for a fiber boost. It worked out wonderfully.


These were really good. I even made them with flax eggs — they kind of retained their original shape on top- so next time I might smooth them out with a rubber spatula first. I will save the recipe!


I just made these and they have a great taste, but are way too dry. Do you think it’s the brand of coconut flour I used? (I used Simple Truth.) I was careful to measure exactly and had all the right ingredients.


    Coconut flour is tricky. I always start with half of what is called for, wait a bit for it to absorb and then add a little more till the right consistency is achieved. In this recipe I used 3/4 of the 3/4 cup with my brand of CF.


What can be subistuted for the eggs in this recipe?

    Megan Gilmore

    To get a similar texture, you’d probably need to use some sort of flour. Flax eggs won’t work, and arrowroot might, but the muffins will be very flat and dense. Let us know if you experiment with it!


These muffins are delicious and super easy to make!


I like the flavor but they are very dry. Next time I think I’ll add some coconut oil or other fat.


I made the recipe exactly as is and they are amazing! So moist and yummy! I think next time I might sprinkle in a few dairy free, chocolate chips.:)


Hi Megan,

Can I use date paste instead of maple syrup instead?

lesley martinson

can we sub sweet potato?

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