Last Updated on September 17, 2025 by Carrie Korem, FNTP
There’s nothing better than a batch of warm pumpkin muffins on a crisp fall day. These pumpkin muffins are made with coconut flour, sweetened naturally, and dotted with chocolate chips for a treat that feels indulgent yet still supports your health. The texture is light and tender, and they’re perfect to enjoy for breakfast, as an afternoon snack, or tucked into lunchboxes.
I especially love this pumpkin muffins recipe because it uses simple, whole ingredients — no grains, no refined sugars, and dairy-free options if you need them. They store well on the counter for a few days and can be frozen, which makes them great for meal prep.
Why Bake Pumpkin Muffins with Coconut Flour?
Coconut flour can be tricky, but once you know how it works, you’ll love using it for baking:
- Moisture matters: Coconut flour soaks up a lot of liquid. That’s why this pumpkin muffins recipe calls for several eggs. Without enough moisture, coconut flour baked goods can turn out dense.
- Stick to one brand: Different brands of coconut flour can give very different results. I always use Bob’s Red Mill coconut flour for consistent texture.
- Pair with almond flour: Often, coconut flour works well with almond flour to keep muffins soft while using fewer eggs.
- Choose the right sweetener: For a lighter texture, I recommend using dry sweeteners like coconut sugar or maple sugar instead of liquid ones.
How to Make Pumpkin Muffins
Making these muffins is simple and doesn’t take much time. You’ll whisk the wet and dry ingredients and then fold everything into the pumpkin puree and chocolate chips. A quick bake in the oven, and you’ve got fluffy, delicious pumpkin muffins ready to enjoy.
Here’s the recipe:
Ingredients
- 6 large eggs
- 1/3 cup heavy cream (or coconut milk for Paleo)
- 1/4 cup + 2 tablespoons coconut sugar or maple sugar
- 1 teaspoon vanilla extract
- 8 tablespoons unsalted butter, melted (or coconut oil for dairy-free)
- 3/4 cup coconut flour
- 2 teaspoons grain-free baking powder (1 part baking soda + 1 part cream of tartar + 2 parts arrowroot)
- 1 teaspoon baking soda
- 3/4 teaspoon Celtic sea salt
- 1 cup cooked and pureed pumpkin
- 5 ounces mini chocolate chips or chopped dark chocolate
Instructions
- Preheat the oven to 400°F. Line a muffin pan with muffin liners.
- In a large bowl, whisk together the eggs, cream (or coconut milk), coconut sugar, vanilla, and butter.
- In another bowl, sift the coconut flour, baking powder, baking soda, and salt. Add the dry ingredients to the wet and whisk until smooth.
- Fold in the pumpkin puree and chocolate chips.
- Spoon the batter into muffin cups and bake for 15 minutes, or until golden brown on top.
Variations
-
Leave out the chocolate and add pecans, walnuts, or white chocolate chips instead.
-
For a nutty flavor, try adding a sprinkle of chopped nuts on top before baking.
-
Enjoy them plain for a naturally sweet and simple muffin.
Pumpkin is rich in beta-carotene, fiber, potassium, and antioxidants that support your thyroid and overall health. Paired with healthy fats and protein in this recipe, these pumpkin muffins are more than a seasonal treat — they’re a nourishing choice you can feel good about.
Here are some other muffin recipes you’ll enjoy!
Browned Butter Banana Muffins with Cinnamon Streusel
Fermented Sourdough Banana Zucchini Muffins
Blueberry Streusel Muffin
Lemon Poppy Seed Muffins
Pumpkin Muffins with Chocolate Chips (Gluten-free)
I prefer to make my own baking powder to ensure that it’s grain-free. Here’s the recipe: 1 part baking soda + 1 part cream of tartar + 2 parts arrowroot. I make the baking powder in large batches and store it in a glass jar. You can leave the chocolate out of the recipe and substitute pecans, walnuts, or even blueberries.
Adapted from Organic Spark.
- Prep Time: 10 minutes
- Cook Time: 15 minutes
- Total Time: 25 minutes
- Category: Baking
- Diet: Gluten Free
Ingredients
For the Batter:
- 6 large eggs
- 1/3 cup heavy cream (or coconut milk for Paleo)
- 1/4 cup plus 2 tablespoons coconut sugar or maple sugar
- 1 teaspoon vanilla extract
- 8 tablespoons unsalted butter, melted (or coconut oil for dairy-free)
- 3/4 cup coconut flour
- 2 teaspoons grain-free baking powder (see above)
- 1 teaspoon baking soda
- 3/4 teaspoon Celtic sea salt
- 1 cup cooked and pureed pumpkin
- 5 ounces organic mini chocolate chips, or chopped bittersweet chocolate (I used Enjoy Life. Only 3 ingredients and no soy!)
Instructions
- Preheat oven to 400 degrees F and adjust rack to middle position. Line muffin pan with muffin liners. Whisk eggs, cream (or coconut milk), coconut sugar, vanilla and butter in a large mixing bowl. Sift coconut flour, baking powder, baking soda, and salt over a medium mixing bowl. Add dry ingredients to wet and whisk until no lumps remain. Fold in pumpkin and chocolate. Spoon batter into muffin cups. Bake for 15 minutes, until golden brown on top. Cool. Store muffins in an airtight container for 3 days.
Nutrition
- Serving Size: Makes 24 regular muffins or about 36 mini muffins.
Photo Credit: Becky Winkler
Thanks for the tips, Carrie. I don’t have much experience with coconut flour either so I appreciate your insight!
I love the combo of pumpkin and chocolate! They look delicious. I have loved following your grain-free challenge!
I am allergic to coconut. What can I use in place of it?
I haven’t tested this recipe with substitutions, so I don’t know which alternate ingredients will lend the exact same texture and flavor.
These look so good. Can’t wait to try them. Thanks for the tips on using coconut flour. I have just started using it and have noticed that a little goes a long way.
I noticed this calls for 3/4 tsp of the celtic sea salt. That seems like a lot. Is there something different about Celtic sea salt verses regular sea salt? or does it need to be the coarse sea salt – (just thought of that) ? I made the grain free cookies the other day and had to throw them out b/c they were way too salty. Made them again last night with 1/4 tsp and they were just about right although I could still taste a little salt. I did just by fine sea salt so maybe that is it? Thanks!
Yes, Celtic sea salt (or any other unrefined sea salt) makes a difference. Celtic sea salt isn’t as salty as regular processed salt so it can’t be switched out 1:1 especially when it comes to baking. I use the fine ground Celtic sea salt (http://astore.amazon.com/deliciorgan03-20/detail/B000SWTKV0). Another positive, is that celtic sea salt hasn’t been bleached, doesn’t contain any anti-caking agents and has over 80 minerals in it. I usually buy the 5 pound coarse sea salt for everyday cooking (on Amazon) and then I have a small bag of the finely ground Celtic sea salt for baking (the fine ground is more expensive).
Carrie, how does Celtic Salt compare to Real Salt?
So these are for me….what are you guys having?
Thank you for the tips on baking with coconut flour.
I have never even heard of coconut flour! Thanks for the tips- These look delicious!
Your muffins look perfect! I can’t wait to make a batch.
God bless you for your patience with the baking process. All of the things you’ve learned along the way would have been insurmountable obstacles for me. Thank you for teaching us the tricks!
They are in the oven now (unfortunately, we’re having a Santa Ana so it’s too hot outside to be baking but I already had everything ready before I remembered that). It’ll be a good surprise for the kids when they are home from school.
Mmm these sound so yummy!
These sound too good to simply click on read and move on – I HAVE to bake them. Was wondering if someone with a nut allergy can eat coconut flour? I know coconut oil is a no no… when does your grain free finish?
I really don’t know. It think it depends on the person. A friend came over the other day who is allergic to nuts but could have coconut, so I guess it depends. The grain free challenge ended, but I’m going to continue featuring lots of grain free recipes. I love playing with new ingredients!
Coconuts are not nuts. My daughter is allergic to tree nuts and we found this out when we discovered her allergy. Nutmeg is also not a tree nut. 🙂
I’ve been wanting to experiment baking with coconut flour and was eyeing a bag at the store the other day. This sounds like a good place to start.
That’s so interesting. I’ve never even seen coconut flour before, where did you get it?
You can get it at most health food stores, but it’s much cheaper to buy online at Amazon or Azure Standard.
I have found that substituting plain yogurt for cream or milk in recipes, then beating it with the eggs until quite fluffy and then folding into muffin recipes makes them MUCH lighter. Maybe this will alleviate some of the density issues?
That’s a great method and one I use in many recipes. It’s really wild how the flour sucks up any liquid it gets ahold of. I haven’t tried the whipping/folding method with coconut flour. Thanks for the suggestion!
YuuuUm! My friend Katie and I were just talking about how we see pumpkin in everything everywhere now that it is Fall…so I had to smile when I opened up this post and found pumpkin chocolate chip muffins! I LOOOVE pumpkin though…so seeing it everywhere is okay by me!! 🙂 This recipe looks delish!
Hugs,
Gail
Muffins look really good. I normally bake a sweet potato and use in most recipes that call for pumpkin. I must put put heavy cream on my grocery list and then I am in business with these muffins. Thanks for all the hard work you put into these recipes. I loved the chocolate chip cookies you recently posted.
These look divine! I’ve been wanting to make Molly’s Coconut muffins but I’ve been waiting for an over ripe banana, maybe I’ll make these instead. Although, it’s supposed to be in the 90’s today, so I may have to wait for a more “fall like” day.
If I use butter with salt, do I omit the salt or use less? or do I absolutely need the unsalted? I don’t have unsalted.
You can use salted butter, but I’d decrease the salt by 1/4 teaspoon.
I made these for breakfast this morning and they were a hit!! Thanks for posting!
Hey Carrie,
I was wondering if you’ve tried doing any homemade chocolate chips? I looked at the Enjoy Life ones at amazon. I’m sure they’re great, but it seems a bit pricey. Just thinking I could try a version at home that may be cheaper? I know I can’t make everything from scratch, but it’s nice to have a cheaper homemade version if we can’t swing them in the grocery budget. Thanks! Keep the grain free recipes coming. I’m loving this new way of eating. Only day 23, but seeing great benefits.
I understand. Our commissary on base had them so I was able to get a bag at a good price. Another option is to buy a good chocolate bar and then chop it up. Or, I saw this recipe for homemade chocolate chips over at Heavenly Homemakers. I haven’t tried the recipe, but it’s on my list! http://heavenlyhomemakers.com/making-homemade-chocolate-chips-in-detail That’s fantastic that you’re on day 23!! Great job!
Funny you mentioned that. I popped over there looking to see if she had one. I’m going to give it a try however, she mentioned it’s not good for baking, just eating…so it probably won’t work without tweaking. I used to visit her site daily, but going without grains now, I’m looking for more of those types of recipes. I will try your chocolate bar idea though. Thanks a bunch.
I love the texture coconut flour gives to baked goods. these look great!
I just made these after dinner and they are sooo good!! Not dense at all. They turned out super moist and a great flavor. I adore chocolate and pumpkin-perfect combo! I already ate two…hopefully I can stop myself before the kids come in from outside! Thanks so much!!!!
We have really enjoyed your grain free living…. I am married to a pilot with 2 small kiddies at home so the ease of following your meal plans plus the bonus well being from grain free living makes it easier when he is gone for extended periods.
Your recipes have been delicious and quick and easy to incorporate into our lifestyle with your grocery lists and allows us to plan to be grain free without the extra steps of planning it ourselves.
My question is will you be continuing to be grain free yourself, and will you be continuing the grain free recipes for those on your meal plans.
Awesome. Awesome.
Thank you for helping us to set a great course for ourselves here in my home!!
In good health, warmth and much light….
Shell
Wow – my daughter and I just made these and it will be hard from keeping my family from gobbling them all up immediately. This is the first recipe I’ve used with coconut flour and I’m glad it was such a success. Thanks so much for all of these wonderful recipes!
I lost. My family ate them ALL!! Ok, we gave 4 away to friends :). As my kids say ” A do-over, mom!”.
Great tips for using coconut flour. I have fresh pumpkin waiting in the frig for these muffins.
Interesting info. on coconut flour.. now I’m intrigued to try it out!
Question: when you (or other recipes) call for coconut milk, are you referring to canned coconut milk, or the beverage/drinking kind, like So Delicious brand?
I use canned coconut milk rather than the beverage/drinking kind. I buy Native Forest coconut milk. It’s organic and doesn’t have BPA in the lining of the can.
Hi, I just made these these on Saturday afternoon and ate the last one this morning (Monday)! I’m thinking about making more tonight since I gave half of them away. They are so delicious!! Thanks for the great recipe.
I made these this weekend, I replaced the chocolate chips with walnuts, YUM! I had some leftover Maple Cream Cheese from making the carrot cake cupcakes, my husband slathered it on and wow did that make these muffins sweeeeet (in a good way)!
Very good, light, easy to make and nobody even knew there was coconut flour in them. I secretly put 6 in the freezer, too 🙂
Nice tips on coconut flour. I’ve been using it for years and love it.
I think I might try these with raisins instead of chocolate.
Carrie, Kelli made these yesterday but used coconut milk and gluten free flour. Absolutely outstanding….I think next time she’ll try the coconut flour. Thank you!
These muffins look great & I am never opposed to too much coconut flavor so bring it on!
These sound great Carrie! I love that you used coconut flour too. I can’t wait to try these. And great tips on coconut flour. It can be a little tricky to bake with. 🙂 And I just might have to try the banana coconut muffin recipe. I have ripe banana’s sitting on my counter that would be perfect. Thanks Carrie!
Hi Carrie- I have made your pumpkin version of these muffins several times (using freshly roasted pureed pumpkin) and they are absolutely delicious!! This morning I tried the banana version from the link you mentioned and they are also good, but I agree with your decision to cut the salt a bit! Wish I had paid attention to the changes you made before I baked today! Thanks for the introduction to coconut flour. Who knew?!?
Just tried this recipe last night. This is the first gluten free muffin recipe that has been anything near as good as wheat ones. I am so pleased to say this is my new favorite muffin recipe…gluten free or not! Thanks for sharing…I’m sold 🙂
I made these last night and only have 2 left as of now. My family loved them. Great recipe! I used dark 60% Cacao chips which was a great bittersweet taste with the muffins.
Followed the recipe as described but added 1tsp of cinnamon, 1tsp nutmeg, 1/2 tsp ground cloves, and 1/4 tsp of ground ginger. SOOOOO tasty! I made a dozen muffins without chocolate chips and a 1/2 dozen with chocolate chips. Will definitely make these again! Thanks for posting.
I like the addition of the spices! Yum!
Do you have a brand of baking soda that you trust? And if you are going to buy your own baking powder is an aluminum free one the best option?
I use arm and hammer for baking soda. For baking powder, yes, it’s best to pick an aluminum-free version, but if you’re trying to avoid grains and/or GMOs then it’s best to make your own (cornstarch is usually used to make baking powder which is a grain and is also usually GMO, unless specified). To make your own just use: 1 part baking soda, 1 part cream of tartar, and 2 parts arrowroot flour.
This is the Aluminum Free Rumford Baking Powder ingredients I was going to order from Azure. Is this OK or should I buy stuff to make my own? I was pleased to see that the cornstarch is non-GMO. I know it is still grain, but at least it is non gmo grain, right?
INGREDIENTS: Monocalcium Phosphate, Sodium Bicarbonate (Baking Soda), Food-Grade Cornstarch (non-GMO)
Yes, that’s a good one. 🙂
Carrie, I don’t know how to thank you enough for all that you do and for sharing it!! You are contributing to changing my eating lifestyle!! And there hasn’t been a recipe so far that I have tried of yours that I haven’t LOVED…I mean it…ABSOLUTELY LOVED! I know it isn’t fall, but I was craving some pumpkin, so I decided to make this recipe tonight, and I had to stop myself because they were so amazing! I even put them in the freezer to help “pace” myself :).
Thankfully, I don’t have any medical reasons or serious problems, but I just wanted to change my eating habits. And interestingly, the more I make changes, and then take a “splurge” down that old path, I can physically feel the nastiness…which of course does nothing but encourage me further down the healthier and cleaner path :). So thank you for all that you do, your allowing us into your life, and for helping to make “living a different lifestyle” so pleasant and enjoyable!
Grateful beyond words!
Toni
Thank you for the kind words. I’m so glad the site/recipes have been helpful for you! I love these muffins too. Hard to each just a few! 🙂
For GAPS, can you delete the baking powder? Will they still turn out or is there another sub that is GAPS friendly?
thanks!!
Yes, you can omit the baking powder. They won’t be quite as fluffy, but they will still taste great.
Hi Carrie,
I was wondering….if I were to use pureed pumpkin from a can, would I use the same amount? Thanks.
Yes. I used pureed pumpkin from a can. Enjoy! 🙂
Thanks for the fast response!
Can I substitute all the coconut flour for rice flour or almond flour and if so how many less eggs can I use?
I don’t have a recipe for pumpkin muffins with gluten-free grains. Sorry I can’t be more helpful.
Can I use salted butter and New Zealand sea salt-pink or white?
Making these right now! 🙂
Salted butter will work, but the muffins will taste more salty, so I’d pull pack on the additional salt in the recipe. And yes, New Zealand pink or white salt will work well. Enjoy! 🙂
Can I substitute coconut oil for butter? We just found out my daughter is allergic to milk. I am so excited to make these for her, pumpkin muffins are her favorite. I am new to baking without dairy!
I haven’t tested it, but it should work just fine. Another great alternative is ghee. Enjoy!
I saw quite a few pleased comments on these on your website so followed your recipe carefully but a little perplexed that they took much longer to bake and were still gooey inside. They don’t taste like much right now but really hoping they will taste better after cooling.
Hmm…I’m not sure why they would be gooey inside. Did you make any substitutions? When it comes to coconut flour, even the slightest substitution or change can throw off the outcome of the recipe.
Thanks, Carrie. My husband cannot seem to give up flour but he loved these muffins as did I. I have loved all your recipes that I have used. Thank you for your hard work.
Sally
You’re welcome! I’m so glad he enjoys the muffins. They are my Dad’s favorite! 🙂
I love these muffins. Last time I baked them, I unintentionally left out the melted butter. Surprisingly, the muffins were still wonderful and delicious. So, I may leave the butter next time.
I’m interested in making these since they are gluten free and look amazing.
I made these yesterday for SAD company and everyone loved them! They are moist, but not soggy. Just the right amount of sweetness. I’m well known for making lots of changes to recipes, but I didn’t change a thing in this one! Thank you for sharing this delicious recipe!
I’m so glad you all enjoyed them! 🙂
Made these this morning. Agree that these are better than the average coconut flour muffin. But it’s still a coconut flour muffin, which isn’t my favorite. I like that these aren’t too moist and eggy, as some can tend to be. These have a vegetable in them and my kids like them, so we’ll probably make them again! Just stashed some in the freezer to take on a trip next week. This made 18 regular muffins, which were actually on the small side.
Glad you enjoyed them! 🙂
I have these in the oven for the second time now, since I can finally make pumpkin muffins (September!) and we’ve been experimenting with eating more grain free. They are so delicious! I made your blueberry coconut flour muffins a few times, and while they are good but I couldn’t quite get over the coconut flour spongy texture. I think because these are more dense, they seem like a completely ‘normal’ muffin to me. I’ve been using coconut oil and honey and they’ve turned out perfectly. Thank you! This batch is half pecan and half homemade chocolate chip. Yum!
Great Coconut Flour explanation. I love baking with it, but explaining it to people can be hard.
Tasty muffins too!!
Just made these today and hubby loved them! It’s perfect for Pumpkin Everything Month, lol. I’m going to refrigerate them for weekday to go meals (especially with our coffees). It was super easy to make and didn’t call for any weird or exotic that I would only use once. I did add some pumpkin pie spice to it for added kick. Thank you for sharing this recipe and tips about the coconut flour!
I used organic pumpkin pie mix in a can BPA free. Is that ok? It was all I had
That will work just fine!
Can’t wait to make these! All ingredients are on the counter awaiting their meet and mingle together however, what can be subbed for coconut sugar or maple sugar? I have turbinado, would that work?
That will work! 🙂
Made these today but I used a level ice cream scoop and only got 16 and baked an additional 4 minutes. They turned out wonderful.
I just made these and they are delicious. I followed the recipe exactly only I added the spices that typically go along with pumpkin. They look just like the photo, thank you so much!
I’m trying to eat low-carb. Is the sugar there just for taste, or is it needed for texture? If the latter, how much do you think I can cut back on it without noticeably damaging the texture?
It’s for both. I reduce the sugar as much as I can in each of my recipes without compromising flavor/texture. I really don’t think you can pull back any more on the sugar in this recipe without changing the texture or flavor.
We substitute Monkfruit without any problems. I start with half of what is called for and then taste. Half is usually perfect.
Hi, you mentioned in the post before the recipe that you like to make your own baking powder but the recipe calls for baking soda only. Want to make sure it isn’t meant to be baking powder.
Thanks
The recipe calls for both baking powder and soda. 🙂