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.

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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 or these Pumpkin Protein Muffins!

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. 5 stars
    I’ve been making these for a while and my husband loves them. The texture is perfect! Today I tossed in a few dried cranberries and realized these muffins really lend themselves to additions. But you can’t beat them plain and hot right out of the oven!

  2. 5 stars
    I love these! I doubled the recipe and they came out great! Half spelt half wheat (all the spelt I had) I didn’t have pumpkin pie spice so I used cinnamon, ginger, all spice and a little cloves. (I don’t care for nutmeg) thank you for sharing this amazing recipe! Not too sweet but sweet enough! Love love love

    1. While we recommend Frontier because it is all-natural, non-GMO, and is a member-owned co-op, the brand you have should be okay. – Nicole

    1. One of our readers added applesauce to make it a little moister. You can add vanilla extract or a little more honey for sweetness. – Nicole

    2. I double the recipe, bake in a Bundt pan, and then add a layer (or 2!) of a cinnamon-brown sugar-butter mixture to put in between bread layers and it adds a little more sweetness and is a fun surprise!

  3. Leona Bertrand

    5 stars
    Made these muffins without any adjustments. I never knew spelt flour could produce such soft tasty muffins. I’m going to use this recipe pretty often… Thanks!

  4. Hello!
    Has anyone ever tried a substitute for the eggs in this recipe? If so, what have you used & how did they turn out?

    1. While we haven’t tried it without egg, a lot of the time banana or apple sauce can replace eggs when baking. If you try it, let us know. – Nicole

    2. I have made these several times using chia seeds as substitute for egges and they come out great!! Just put a spoonful in the grinder, or blender, and break them up, mix with a little water and let it set for about 5 minutes. Sub 1 tbls for 1 egg!!

  5. 5 stars
    I always make these muffins as a double batch for freezing. I was low on canned pumpkin today and completely out of pumpkin spice. I altered the double-batch recipe with no added sugar applesauce and substituted cinnamon. I think they turned out even better than the original (gasp!) – a touch sweeter and a hint of apple.

    Try it:
    Double the quantities of everything in the original recipe but modify items below:
    2 TBS cinnamon (instead of pumpkin spice)
    1 cup of pumpkin
    1 cup of applesauce (new twist!)
    3 eggs (did not double eggs since applesauce consistency adds liquid)

    Mix and bake according to original recipe. Enjoy!

  6. 5 stars
    The pumpkin pie spice used to take you to a homemade recipe. Now the link takes you to an amazon premade spice. Can you post the original pumpkin pie spice recipe? I love the muffins but we always made it with your original spice.

    1. 5 stars
      I’m really new to eating whole foods and I’m quite clueless about all of it. Can you tell me which dark chocolate is best to use? Is it considered a whole food?

      1. Amy Taylor (comment moderator)

        Hi there. Look for an organic dark chocolate with a low ingredient list.

  7. 5 stars
    I made these muffins the other day, and they turned out amazing! I only had 1/4 cup of honey at the time, so I used a little under a 1/4 cup of maple syrup and a squirt of stevia to compensate for the rest. Everyone loved them. Gonna try a pumpkin banana variation today (not enough pumpkin) and see how they turn out.

  8. 5 stars
    Very yummy recipe!!! I was looking to cook some pumpkin muffins today, and this recipe has just the right amount of sweetness I was looking for! I don’t eat clean sometimes but I try to when I can! Thanks so much!

  9. How can I determine the nutritional value for these wonderful muffins? Can you also recommend a good whole grain bread to try?

    1. Amy Taylor (comment moderator)

      There are online tools that can help you figure out those details such as My Fitness Pak and many others. Food for life’s Ezekial bread is a good choice.

  10. 5 stars
    I would love to see more recipes using spelt flour. Nature’s Legacy used to be called Vita Spelt and it’s what I’ve cooked with for a number of years when we discovered that my son is allergic to wheat (not gluten intolerance – actual wheat allergy). I usually used their whole grain white as I could make things for him that he would eat more readily than the whole grain spelt. I would love to cook with spelt all the time – it tastes so much better! Can’t wait to try this recipe!!

  11. You may want to try these using buckwheat flour. I use it for pancakes and breads so this is going to be my next recipe to try.

    1. 5 stars
      I was skeptical that these would be too dry or dense as that usually happens to my baking when using Spelt…… not this time ! The butter and honey have created a beautiful soft buttery texture . I made these as mini muffins for school
      Lunches and added choc chip no other alterations to the recipe . The kids devoured them ! This will be my go to pumpkin muffin recipe from now on .

  12. I’m wondering if I can use agave instead of honey? Nothing against honey, i just have agave and am trying to get rid of it.

    1. Amy Taylor (comment moderator)

      Hello. We don’t use agave in our recipes so I can’t advise on its use. We only use honey, maple syrup, and occasionally a bit of sugar.

  13. 5 stars
    My super picky preschooler ate 3 of them. Literally licked his plate. I subbed applesauce for butter, maple syrup for honey. They were moist and cake like and easy to make. Not very sweet, which I didn’t mind, but thought my son wouldn’t like them because of that. I was wrong! Yay! I think it was the texture that sold him on them. Now he’s asking for green muffins, so I’m going to try spinach/banana muffins.

  14. I love these muffins! I modified this recipe to use 1/3 c egg white instead of whole eggs and 1/3 cup organic, unsweetened applesauce instead of butter. I also used 1/2 c pure maple syrup instead of honey which brings the grams of sugar down. They are still delicious. Moist and cake-like and the maple and apple add a complexity to the flavor. Brings them from 7 weight watchers points down to 3.

  15. Just made these with my boys. In oven now. Subbed maple syrup, coconut oil and added some currants and hemp hearts. Excited for our dessert and snack tomorrow

  16. Can you use stevia in place of the honey and if so how much. I read that real honey is not actually sold in stores and if you want pure honey you should get it from a bee farm. It does not look as pretty as the honey sold in stores. Any advice is much appreciated.


    1. Amy Taylor (comment moderator)

      Hi. We really don’t use stevia in our baking. As for honey, if you buy raw honey, you are buying quality honey with all its enzymes in tact. You can find it at stores like Whole Foods but most larger mainstream grocery stores have it, too. Even better, look for local raw honey at your farmer’s market.

      1. Amy Taylor (comment moderator)

        We really don’t use stevia in our baking so I can’t guide you as to an amount.

  17. Could you possibly supply gluten free substitution in you muffin and bread recipes? I’ve recently purchased coconut, oat, and almond flours and would love to make some “real food”, power-packed snacks and quick breakfasts. Thanks (different Shannon)

  18. These were delicious!! Love the cake like texture- added chocolate chips and they made a perfect after dinner treat! I love spelt flour- I think it tastes much better than whole wheat. :)

  19. I made the muffins but I was a little concerned because the batter was a little stiff. They baked in exactly 18 minutes and they are delicious. I substituted coconut oil for the butter. Perfect

  20. 1 star
    I’ve used a similar recipe for ages. I use 1 tbsp canola and 2 tbsp applesauce for the fat, a 1/4 cup more honey + 1 cup shredded carrot. You barely notice the carrot, but adds more vitamins and fiber! Yum!

    1. 5 stars
      Oh, I see you don’t use canola. That oil isn’t really necessary…that’s just the way the recipe was when I found it, so it’s what I’ve stuck with :)

  21. Made these at the weekend and my kids loved them! We can’t get hold of pumpkin purée easily here in England, so I used sweet potato purée instead. Delicious and so moist! The sponge reminds of of Jamaican ginger cake, so I am going to flavour these with more ginger next time. Thankyou for the recipe!

  22. 5 stars
    Hi, Could I get the nutritional values for these muffins?
    Calories, sat fat, protein, fiber, sugar etc? Thanks!
    Really love this recipe!