Healthy Pumpkin Muffins Recipe

55 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.

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.

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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379 thoughts on “Healthy Pumpkin Muffins Recipe”

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Recipe Rating

  1. 5 stars
    I have made 2 different variations of these muffins for my kids school lunches and they love them! For my son who likes blueberry muffins I substitute applesauce for the pumpkin and add blueberries, cinnamon and nutmeg. (No pumpkin pie spice) For my son who likes banana muffins, I substitute mashed bananas for the pumpkin and leave out the spices. I really like adding walnuts to them also. So good!!

  2. Are there any baking powers without cornstarch or aluminum? I was surprised to find these ingredients in the one I’ve been using for a long time.

    1. The Whole Foods 365 brand does have corn starch but is aluminium free. I just read that says you can make your own baking powder by mixing one part baking soda with 2 parts Cream of Tartar. I haven’t tried it but it might be worth a try.

      1. Thanks! Question… Do you have nutritional info on these (specifically how much protein and sugar in each one)?

      2. Thanks! Love these so much!! Question… Do you have nutritional info on these (specifically how much protein and sugar in each one)?

  3. I followed the recipe exactly and they are wonderful!! My kids and my husband loved them! Thank you for such a wonderful recipe!

  4. 5 stars
    We make these all of the time! I add raisins once in a while too. We have 5 kids and each and every one of them love these! They freeze well too

  5. This is my new favorite, easily doubled, all in one bowl and freeze great! Husband loves them. I used fresh roasted pie pumpkins…so good. Five stars for sure.

  6. Could I substitute mashed banana for the pumpkin (and leave out the pumpkin spice)? Trying to come up with a different variety for my boys. I’ve never baked with spelt before and loved the texture! Thanks!

  7. 5 stars
    I was so excited to try to make these last night. I had leftover pumpkin from making pumpkin chocolate chip muffins last week, so got all ready to mix these up last night. Mixed all ingredients and got ready to mix in my pumpkin, but opened the container and realized it was SPOILED! EEK! so I had a bowl of this muffin mix, what was I to do!? To improvise, I added 1/2 cup applesauce, handful of raisins, and about a cup of ALL bran cereal …mixed it all together and hoped for the best. While i was disappointed that I didn’t get the pumpkin muffins, my apple raisin bran muffins are fabulous!! I love the spelt flour- first time I’ve baked with it, and it truly is much lighter! Thanks for the recipe! next time I really will do the pumpkin! :)

  8. I love pumpkin muffins and this is a much healthier recipe than what I usually make. Can’t wait to try them!
    Can you explain the process of freezing and thawing the muffins?

    Thank you!

    1. Amy Taylor (comment moderator)

      Hi there. After the cooked muffins have completely cooled, put them in an airtight container or bag to freeze. When you are ready to defrost, just place them in the fridge overnight.

  9. I would like to make many of the muffins on this site but they mostly have honey in them. I am making them for my 9 month old and I have been told no honey before 12 months. What can I substitute? I have maple syrup?

  10. Can I substitue sweet potatoes instead of pumpkin? Would I do a different kind of spice, or keep it the same?

  11. I have made these muffins dozens of times & decided to try almond flour. I followed the instructions (per the manufacturer) to use half the amount of almond flour & the muffins came out totally deflated. Any ideas as to why?!?

  12. I have made these muffins a few times and they are delicious!! My only problem is the last 2 times I made them, they came out with an unwanted crunch or gritty piece in very couple of bites…almost like an eggshell but there wasn’t…? Had anyone else had this problem? I thought maybe it was the canned pumpkin I used but this time I switched brands and it still happened :(

  13. 5 stars
    I use organic whole spelt flour for the majority of my baking at home since everywhere else I go the options are always white or whole wheat. I figure it’s good to switch things up a bit! I love that spelt is light and also whole grain. I also sometimes mix it with a multigrain flour or buckwheat etc. These pumpking muffins are delicious! My favourite I’ve tried on this site so far. I’ve heard a few people suggest subing the oil for apple sauce so I might try that next time to see how it turns out. Thanks for all of your recipies! My (unborn) baby is very appreciative! :)

  14. What happened to the whole spelt lemon cottage cheese pancake recipe? :( it’s gone. I have cottage cheese I intended to use up with this recipe. Is it posted elsewhere? Thanks!

  15. 5 stars
    I made these the other night but used the whole can of pumpkin since I knew it would go to waste otherwise. They turned out great and even my 12 yr old loved them. This is the first time I have used spelt and will definitely be using it again!

  16. 5 stars
    This has become a family-favorite, but because of a life-threatening milk allergy in one of our children, I’ve made a few substitutions. I wanted to share them with you in case other readers might need to do the same.

    First, the recipe doubles perfectly (clearly we love them – I can’t make a single batch!). I sub equal parts melted coconut oil for the butter – and also used 1/2 almond flour in place of the whole wheat flour. They come out perfectly ever time!

  17. 5 stars
    Thanks for this great recipe! The family has enjoyed everything I have made from 100 Days of Real Food :D Great to know that there are recipes that are both healthy and delicious.

  18. Do you have other favorite uses for spelt flour? We finally found it (and love these muffins), but I’m wondering what other recipes might benefit from use of this type of flour?

  19. Hi Lisa, I made these whole spelt pumpkin muffins last night and they were INCREDIBLE! I’m diabetic, so I subbed the pumpkin and honey. Instead, I used sweet potato puree and agave. I was amazed by how easy they are to make, but how incredibly delicious they turned out. The secret is the pumpkin pie spice; I made my own spice following the link you posted on the ingredient’s list. I suggest everyone to never leave this ingredient out, it makes the whole difference.

    Thank you for the recipe Lisa!!

    Greetings from Madrid.

  20. I made these muffins tonight and added raisins, which got me 2 more muffins. Yay! They’re SO good!! P.S. I used whole wheat flour because i didn’t have spelt flour, and they turned out great.

  21. I followed the recipe as is, but made them as mini muffins. The baking time was 10-12 minutes for my oven. They turned out pretty good. Thank you so much for providing the pumpkin pie spice, I always hate searching for that on the net or at the store :)

  22. 5 stars
    Made these muffins tonight with 2/3 whole wheat flour, 1/3 regular flour, and 1/3 honey, 2/3 maple syrup (ran out of honey). I doubled the batch. They’re great! They’re exactly what I was looking for in a muffin for my toddlers. I wanted something that was not a dessert but rather something I could give them for breakfast or as a healthy snack. Perfect!

    1. Amy Taylor (comment moderator)

      Hi Chris. I’ve successfully replaced it 1:1 but more often use half coconut oil and half applesauce. :)

  23. Hi…I’ve been looking thru the comments to see if a suggested cooking time has been discussed for making these as mini muffins. Not seeing a comment about this. What do you suggest?

  24. 4 stars
    I made the Pumpkin Spelt muffins this morning. While the texture and moistness was perfect, I was hoping for more of a pumpkin taste. Would doubling the pumpkin pie spice help?

  25. I just made these but used whole wheat flour and they are so delicious!! I’ll be bulk baking these to freeze for sure!

  26. Just made these with fresh pumpkin purée from pumpkins I picked at a local farm. These are my new favorite muffins! The carrot applesauce were my favorite, until I made these. Delicious, moist, and just the right amount of sweet. I made a double batch and will be throwing them in the freezer.