Healthy Pumpkin Muffins Recipe

57 Reviews / 4.9 Average
These pumpkin muffins are easy, healthy, and delicious with a cake-like texture (the secret is in the ingredients!). Perfect for the holidays or anytime. They are also freezer-friendly, so make sure to bake a double batch!
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Basket of fresh baked Pumpkin Muffins.

I finally did it! I’ve been wanting to bake with some alternative flours for some time, and this weekend I finally made this pumpkin muffin recipe using whole spelt flour. And I must say, they are deeeelicious! We’ve definitely been missing out … the texture is much more cake-like and the taste is milder than regular whole-wheat flour.

It was super easy to make the 1:1 substitution … I have no idea why I kept putting it off! But if you don’t have spelt flour you could definitely use whole-wheat pastry or regular whole-wheat flour instead.

For a gluten-free option, make this Healthy Pumpkin Bread!

Baking Tips

This recipe is super simple to make and it would be really fun to kids to help out. Best of all, you can make the batter in just one bowl—less to clean up! I recommend making a double batch of muffins to have ready in your freezer for a quick breakfast or school snack on busy days.

You can also bake these in mini-muffin tins if you’d like (be sure to check them at around 10 minutes) or bake them in festive muffin cups or paper liners depending on the holiday or season.

For more baking tips, check out this Teaspoon to Tablespoon Conversion!

Pumpkin Spelt Muffins sitting on a white cake tray.

What Makes These Pumpkin Muffins Healthy?

Whole Grain Flour

Spelt may sound like a “new” grain (at least it did to me), but it’s actually been around for more than 9,000 years. As I mentioned, the flavor is “lighter” than wheat and even though it contains gluten, some with an intolerance to wheat find that they are able to enjoy spelt.

Just like with wheat though, you want to be sure to select “Whole” spelt products as opposed to the refined (white) version. And to keep your whole spelt flour fresh, it’s best to stick it in the freezer (or fridge) along with your other whole grain flours.

Natural Sweeteners

When it comes to sweeteners, I use the least processed sweeteners available, which are honey and 100% pure maple syrup. You won’t find any refined sugar in these muffins. But, like with any recipe that calls for sugar or sweeteners, moderation is key … because “sugar is sugar” no matter how you look at it (learn more in my “Sweeteners 101” post).

Can I Use Halloween Pumpkin?

The simple answer is yes. Once you’re done carving your pumpkin for Halloween you can turn it into pumpkin puree, but there are some major differences between your jack-o-lantern and a “pie” pumpkin that you might want to consider. 

One of the most common methods of homemade pumpkin puree is roasting it, so a large Halloween pumpkin might not be the best size to fit in your oven. They are also a lot more stringy and have less flesh than the baking ones. And from my experience, the flavor just isn’t the same since carving pumpkins have less natural sugar, resulting in less sweetness for those yummy fall desserts. 

By all means, you can still turn those festive Halloween pumpkins into a puree if you’d like, but I definitely recommend using a smaller pie pumpkin for the best outcome. Whichever you choose, try one of these two simple methods we explain in this post

Pumpkin Puree Tip

If you use canned pumpkin, make sure you purchase a can of pumpkin puree and not pumpkin pie filling. While they may seem similar, pumpkin pie filling is a blend of squash, sweeteners, and spices—and I’ve already mentioned how I like to stay away from refined sugars!

What Is Pumpkin Pie Spice?

Whether it’s the famous Pumpkin Spice Latte or a holiday Pumpkin Pie at Thanksgiving, the main flavor is Pumpkin Pie Spice. This fall flavor is generally a blend of cinnamon, ginger, nutmeg, cloves, and sometimes allspice. You can find a variety of store-bought blends or easily create your own using these measurements (makes about three ounces):

  • 3 tablespoons ground cinnamon
  • 1 1/2 tablespoons ground ginger
  • 1 tablespoon ground nutmeg
  • 1 teaspoon ground allspice
  • 1 teaspoon ground cloves

How to Store Pumpkin Muffins

After you’ve let the muffins cool completely on a wire rack, transfer them in a single layer into an airtight container and store them at room temperature for up to 4 days. 

If you’re worried about soggy muffins, one trick is to line the bottom of the container with a paper towel, add the muffins, then place another paper towel on top. This is supposed to help absorb any moisture, resulting in your muffins staying fresher, longer. 

As I mentioned before, I always make a double batch of any kind of muffins to store in the freezer. They are a great time saver for school lunches, on-the-go breakfast, or snacks. 

For these pumpkin muffins, or any bread item, there are two ways you can freeze them:

  1. Freeze them in one layer on a baking sheet. Then once they are frozen, transfer them to a big Ziploc bag or other freezer-safe containers. 
  2. Eliminate a step by separating the layers of food with pieces of wax paper in your freezer-safe container/bag (so nothing sticks together). With certain foods (like muffins) I find that I don’t even need the wax paper.

I recommend only storing them for up to 6 months this way. When you’re ready to enjoy them, take your desired amount out of the freezer the night before and let them defrost in the refrigerator overnight, or on the counter at room temperature. If you’re in a hurry, you can always pop it in the microwave for a few seconds, too.

Video: How to Make Pumpkin Muffins

I was in LA and got to visit Catherine McCord (of Weelicious) in her kitchen where I showed her how to make these muffins. Check it out in the video below!


More Pumpkin Recipes

More Muffin Recipes

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Recipe Rating

  1. I’ve roasted and puréed my own pumpkin but how much of the purée should I use? The recipe just calls for a can of pumpkin but doesn’t say what size the can is.

    1. Amy Taylor (comment moderator)

      Hi Lisa. Look for a grass-fed butter: Purity Farms Organic Ghee, Organic Valley, and Kerrygold are a few examples. :)

  2. I just made this recipe, but used carrots instead of pumpkin, and coconut oil instead of butter, and it is SO GOOD!

  3. I make these pumpkin muffins almost every week (during fall) and my kids never get tired of them. This week I made them for my birthday – added (homemade) cream cheese icing :) We devoured them! Even though frosting was made with regular sugar it was great to know the muffin/cupcake was organic and whole grain and made with no processed sugar (I bake w/ maple syrup) — nice health compromise…but NO compromise on taste/flavor/enjoyment. My daughter is now thinking about making the lemon raspberry muffins w/ frosting (of course) for her birthday.

  4. I just made the lemon cottage cheese pancakes with blueberry lemon syrup. Licked my plate clean!!!! Delicious! Thank you for a great recipe. It made about 5 pancakes and 1/2 the syrup recipe was the perfect amount. I failed at whipping the egg whites but it didn’t matter – they were as plump and even more moist (thanks to the cottage cheese) than any pancake recipe I’ve made before. Definitely putting this recipe in the keeper pile….along with your slow cooker baked beans. :)

  5. So, instead of using the King Arthur’s Organic White Whole Wheat Flour you are substituting the spelt? I went the page you linked for more info, and it was recommended to decrease the water when baking with spelt. Did you alter your recipe in this way or just do the 1:1 sub? I’m just really wondering about all the recipes I have that use flour and making tortillas with the spelt. Have you tried that? Thanks!

    1. Assistant to 100 Days (Amy)

      Hi Andrea. I’ve always subbed them 1:1. I must have missed the water footnote :) but have never had an issue. I have made tortillas with spelt quite successfully, too. You could always reserve a little water and add as needed. ~Amy

  6. 5 stars
    I made a few changes…whole wheat pastry flour, flax egg, coconut oil instead of butter, and maple syrup instead of honey. I also added some dark chocolate chips! they are amazing!!

  7. 5 stars
    I love this recipe and make it all the time. Today I didn’t have canned pumpkin (the 100% organic canned kind) but I had a pie pumpkin so I trimmed off the “skin” and cut it into pieces. I roasted it with some drizzled coconut oil for 20 minutes at 325 degrees. Afterwards I puréed it and made my own pumpkin purée and it was even more amazing. Definitely recommend trying it.

    While that was roasting I was busy maing the other muffin recipe I found on here for lemon raspberry muffins. The timing was great!

  8. Hi
    I just the spelt pumpkin muffins and they are quite dense. Ive tried several other bread/muffin recipes like zucchini and those also come out dense. Is that the way they are supposed to be? What accounts for it? How can I make them so they are lighter?
    Thank you

    1. Assistant to 100 Days (Amy)

      Hi Lia. Whole grain flours makes for a more dense bread. You might try white whole wheat which can bake up a little lighter. It is still 100% whole wheat. ~Amy

  9. 5 stars
    I make these year round and I love them! I read about some people getting 6 muffins out of this recipe. Maybe if you use large muffins tins, sure. But I have always gotten 12 muffins from this recipe using a standard muffin pan. I can’t wait for fall time so I can make these for all of my neighbors! Thanks!

  10. I made the spelt pumpkin muffins 3-4 weeks ago — using only cinnamon, ground ginger and cloves in roughly 1/2, 1/4 and 1/4 proportions to one another for the pumpkin pie spice (b/c I don’t love nutmeg) and adding chopped walnuts to the batter before baking. They were absolutely delicious! This recipe is going into my regular breakfast rotation. (Going to try lemon blueberry next for spring/summer. . . .)

    Thank you!

  11. Just tried this recipe for first time. My daughter loves them. I even cut the honey done by 25%. I got 12 perfect sized muffins from this recipe.

  12. These turned out great! I have to say I made more substitutions than I intended to because of ingredient availability. I substituted: 2T flaxmeal:6T water instead of eggs, 4T maple syrup instead of honey, and added 1/2 banana for moisture. Cooked for 15 minutes in mini muffin tin, made 30 muffins. I have never used spelt flour before and the texture IS light and fluffy. I will make these again.

  13. 5 stars
    I’m in love with the pumpkin muffin recipe. I’ve been baking a lot of muffins recently for a quick go-to in the mornings, and this is by far the easiest and tastiest I’ve come across – thank you so much! I love the minimal ingredient list, using honey instead of sugar, and of course they taste great! My picky husband and twin toddler girls love them as well. Thanks so much for a breakfast staple in my home, I hope to see many more muffin recipes to come. 

  14. Just made the muffins yum! Didn’t have pumpkin pie spice so used clove,nutmeg, ginger and cinnamon. I doubled recipe except for honey and added a small amount of semi sweet chocolate chips and subbed 1/2 butter for Greek yogurt. Boy were they moist. My daughters who always hate pumpkin saw the gooey chocolate and couldn’t resist!

  15. Whole spelt lemon cottage cheese pancakes……ABSOLUTELY AWESOME! Even got the man to eat them and he loves them! Woo hoo! Thanks Lisa!

  16. Do you know if there is a difference between American and Canadian whole wheat flour in regards to baking? I know there is a difference in the way ours (Canada) is made, but I wasn’t sure if that affected the baking. The first time I made this recipe I followed it exactly with all brand new ingredients substituting the spelt flour for soft whole wheat(our version of white whole wheat I think). The batter looked like cookie dough and turned into hard little rocks when I baked it. I tried it with only 1 cup of whole wheat flour and I got 12 perfect muffins. Just wondering if any of your Canadian followers have had similar experiences.

    BTW They were soooooooo delicious!!!

  17. My son has an egg allergy. Have you tried the Spelt Pumpkin Mufffin recipe with any egg substitutes? Any recommendations? Thank you!

    1. Assistant to 100 Days (Amy)

      Hi there. Some possibilities for substituting for one in baking are:
      1/4 cup of applesauce (or other pureed fruit)
      1/2 mashed medium banana
      1 tablespoon ground flax seed mixed with 3 tablespoons warm water
      Hope that helps. ~Amy

  18. Thanks for mentioning in the video that you can substitute coconut oil for butter in this recipe. I am going dairy free while nursing my daughter, and was bummed about the melted butter until I saw the video.

    1. Assistant to 100 Days (Amy)

      Hi Keri. You may be able to incorporate some coconut flour but it soaks up so much moisture that I think you would have to completely reinvent the recipe. ;) ~Amy

  19. 5 stars
    i love the pumpkin muffins. i made mine with oat flour (i personally just ground up some old fashion oats) and they turned great. my 19 mo old even loved them.
    thank you for this site and recipes. my family and i are working to eat cleaner and you are a great help!!

  20. Hi,

    I am in Australia and we don’t have pumpkin spice. Is there a recipe or what are the ingredients? Also your pumpkin puree: What pumpkin do you use to make the puree?

    1. Assistant to 100 Days (Amy)

      Hi there. Pumpkin pie spice is cinnamon, nutmeg, ginger and allspice combined. The pumpkin puree we use is generally an organic canned pure pumpkin puree, though you could puree your own from a fresh pumpkin. ~Amy

  21. 5 stars
    Made these for breakfast this morning. This was the first time I have used spelt flour and loved the results. The texture was not dense at all and actually was fluffy. These were not too sweet but just sweet enough. Great recipe!

  22. I have a child who won’t eat anything pumpkin. Have you tried this recipe with any other fruit? Was thinking of substituting cinnamon for the pumpkin pie spice blend and little apple chunks for the pumpkin puree. Does that sound like it would work?

    1. Assistant to 100 Days (Amy)

      Hi Susan. Since that is not something we have tried, we can’t say for sure. We love, however, when people experiment and let us know how it goes. :) ~Amy

  23. HI, I only got 6 small muffins out of the spelt recipe above- not sure why, but its rather annoying to go to the trouble of baking for such small quantities!

    1. Assistant to 100 Days (Amy)

      Hello Jodi. Not sure what happened but you should have gotten at least a dozen. I usually have enough batter for 13 or 14. ~Amy

    2. I just made these and only for 6 muffins as well. I substituted for oat flour and coconut oil instead of butter. Do should be the same quantity. Definitely not a mixture for 12. Thank you for the recipe.

  24. The pumpkin muffins ARE awesome!! I just used regular whole wheat flour and it turned out perfect. I have made it twice now, and the kids request it all the time. Thank you!

  25. 5 stars
    just a note that I made these muffins the other evening & I couldn’t bare to not use my entire (15 oz) can of pumpkin…I always struggle to use up the leftovers. So I went ahead and added all the pumpkin and then an additional dash (tbsp or so) of spelt flour – they turned out great! My new favorite muffin recipe (other than the carrot/applesauce muffins). Thank you for all you do — 100 days is my go-to for all things food :)

  26. My kids and I love these pumpkin muffins. I think they would be a great gift for our church leaders, and I thought it would be cute to bake them as little bread loaves in tins. Any idea how long I would need to bake them for? I am new to cooking and baking all around, but thanks to this blog I have started cooking in order to feed my family, and friends, healthier foods. Thank you!

    1. Assistant to 100 Days (Amy)

      Hi Shannon. You would need to up the cook time a bit. And, it depends on the size of the loaf. I have tiny loaf pans about the size of two muffins. I would toothpick check them after 25 minutes and go from there. ~Amy

  27. So I’ve been making this recipe for about a year now and love it. Today I tried sobbing yogurt for the pumpkin and added chocolate chips. Came out GREAT. Just FYI. I imagine one can use applesauce for vegans. Nice job with this recipe 100days. So versatile. :)

  28. Hi! I was thinking of doing one tablespoon cinnamon and mashing bananas up instead of you know how many bananas I should mash for this recipe? Thanks!