Pumpkin Muffins with Chocolate Chips (Grain Free, Paleo, Primal)

Baking with coconut flour can be challenging. It soaks up an incredible amount of moisture (that’s why most recipes call for an insane amount of eggs) and can lead to a very doughy and tough baked good. I haven’t baked with it for very long, but have learned a few things along the way.

1. For most recipes, coconut flour works well with almond flour to bind the ingredients together. Using almond flour reduces the required number of eggs, too.

2. If you’re baking with coconut flour and avoid coconut milk or coconut oil in the recipe, your end product won’t taste too “coconutty”. So even if you’re not a huge coconut fan, you might just enjoy the final result.

3. For a less dense muffin or cake, use a dry sweetener instead of a wet one. Instead of honey or maple syrup, reach for sucanat or maple sugar.

4. While it’s a bit more expensive than other ingredients, you don’t need much in each recipe. A little goes a long way.


Last week I was about to make Molly’s coconut banana muffins again and remembered I had just picked up some pumpkin. So I swapped out the banana for pumpkin, made a few other tweaks, and the end result was a moist, light muffin with little specks of chocolate throughout. I ate 3 in one sitting. Terrible, I know. But gosh are they good.

Pumpkin Muffins with Chocolate Chips (Grain Free, Paleo, Primal, Gluten Free)

Serving Size: Makes 24 regular muffins or about 36 mini muffins.

Pumpkin Muffins with Chocolate Chips (Grain Free, Paleo, Primal, 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.


    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!)


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.

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  1. Erin

    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!

  2. Brooke @ Food Woolf

    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!

  3. Stacie

    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.

    • Deliciously Organic

      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!

    • Deliciously Organic

      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!

  4. Gail

    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!


  5. Susan

    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.

  6. Karen

    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.

  7. Sally

    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.

      • Sally

        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.

  8. Amanda

    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!!!!

  9. Shell LeDrew

    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….

  10. 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!

  11. Arlinda

    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.

  12. Karen

    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 :)

  13. 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!

  14. 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?!?

  15. JT

    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.

    • Deliciously Organic

      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.

  16. T

    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)

  17. Toni

    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!

    • Deliciously Organic

      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! :)

  18. Kate Lilly

    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!

  19. jackie

    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.

    • Deliciously Organic

      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.

  20. 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!

  21. Renee P.

    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.

  22. Cait

    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!

  23. Deuce

    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!

  24. Debarana

    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?


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