Healthy Pumpkin Muffins
This post contains affiliate links. Read our disclosure policy.
Healthy Pumpkin Muffins are a delicious refined sugar free treat!. Naturally gluten free – these muffins are easy to make and so tasty!
This post contains affiliate links. This post was shared in 2017 but has since been updated.
These healthy pumpkin muffins might be the best muffins we’ve ever made.
These healthy muffins are naturally sweetened with maple syrup, made with whole grain oat flour and other basic pantry staples. They take less than 15 minutes to prep and are so tsty!
I’ll admit it, I’m one of those people that LOVES pumpkin, so it was easy to fall in love with these muffins. If you love pumpkin, you have to checkout these 34+ Healthy Pumpkin Recipes!
liz’s top tips for healthy pumpkin muffins
- If you don’t have these spices, try substituting with pumpkin pie spice!
- Be sure to grab pumpkin puree and not pumpkin pie filling at the grocery store! Pie filling can be full of sugar and spices.
Ingredients
I love this non stick muffin tin or these silicone muffin liners for baking muffins.
Substitutions
Milk: You can use any milk you like in this recipe. Dairy or non dairy (almond, soy, oat, coconut) will all work
Oat Flour: You can make your own oat flour following this oat flour recipe. You can’t use coconut flour or almond flour in this recipe. I haven’t tried this recipe with whole wheat flour but I think it would work!
Sweetener: You can sub maple syrup for the honey in this recipe.
Add ins: I like adding chocolate chips. Chopped nuts, dried cranberries, or seeds are also delicious.
Spices: You can use 3.5 teaspoons of pumpkin pie spice in these muffins. If you do not have nutmeg or cloves, just add a little bit more cinnamon/ginger.
Pumpkin: If you’re out of pumpkin, you can use mashed bananas. You could also make these Healthy Banana Muffins! I have not tried subbing the pumpkin puree for sweet potatoes, but I think it would work. Otherwise you could try this Sweet Potato Muffin Recipe!
Is pumpkin puree the same as canned pumpkin? Yes! Pumpkin puree and canned pumpkin are the same thing. Make sure you are buying pumpkin puree or canned pumpkin and not pumpkin pie filling. Pumpkin Pie filling has sugar and spices added.
Vegan: I have not tried making these muffins vegan, but you might be able to substitute the eggs with flax eggs. You can substitute maple syrup for honey.
High Protein: We love these Pumpkin Protein Muffins as a higher protein fall muffin (9g per serving).
Bread: I haven’t tried making this recipe into a pumpkin bread, but you can try our healthy pumpkin bread recipe!
How to make Healthy Pumpkin Muffins
- In a large bowl or stand mixer, combine maple syrup, pumpkin puree, eggs, and milk.
- Once combined, add in baking soda, cinnamon, nutmeg, ground ginger and cloves.
- Add the oat flour to the wet ingredients. Stir until just combined (don’t over mix!)
- Gently fold in chocolate chips. Pour batter into greased or lined muffin tins. Sprinkle with extra chocolate chips on top if you’d like.
- Bake at 350 for 20-25 minutes, until a toothpick comes out clean when inserted in the center of the muffins.
- Enjoy with a vanilla latte!
Storage Options
These low fat pumpkin muffins won’t last long in your house. I love to snack on them with a Low Sugar Pumpkin Spice Latte!
Storing: Let the muffins cool at room temperature, then store the leftover muffins in the fridge for up to a week to maintain freshness. You can leave them out of the refrigerator, but they will not last as long because they’re very moist and will get moldy.
Can you freeze pumpkin muffins?
Yes, you can freeze these pumpkin muffins! Allow the muffins to cool, then store them in an airtight container or ziploc bag in the freezer. To defrost, leave out the night before in the fridge and they will thaw out. Or, just pop in the microwave for 1-2 minutes directly from the freezer
Other healthy muffin recipes you’ll love:
We love healthy muffin recipes so much that we created a whole free muffin ebook about them! You can get it here or check out these Healthy Muffins:
Healthy Pumpkin Muffins
Ingredients
- 1 ½ cups pumpkin puree
- ½ cup maple syrup or honey
- ¼ cup milk regular or nondairy
- 1 tablespoon vanilla extract
- 2 eggs
- 2 cups oat flour gluten free if necessary
- 2 teaspoons baking soda
- 2 teaspoons ground cinnamon
- ½ teaspoon ground ginger
- ½ teaspoon ground nutmeg
- ¼ teaspoon ground cloves
- ½ cup chocolate chips
Instructions
- Preheat the oven to 350 degrees F and prepare a greased or lined muffin tin. We recommend using silicone muffin liners or a nonstick muffin tin.
- In a large bowl or stand mixer, mix together the pumpkin puree, maple syrup, milk, vanilla and eggs.
- Once combined, add in the oat flour, baking soda, cinnamon, ginger, nutmeg and cloves. Mix until just combined (don't over mix!)
- Gently fold in chocolate chips.
- Pour batter into greased or lined muffin tins, filling each cup with ⅓ cup batter. Sprinkle with extra chocolate chips on top if you'd like.
- Bake at 350 degrees F for 20-25 minutes or until a toothpick comes out clean when inserted in the center of the muffins.
Video
Notes
- Milk: You can use any milk you like in this recipe. Dairy or non dairy (almond, soy, oat, coconut) will all work
- Oat Flour: You can make your own oat flour following this oat flour recipe. You can’t use coconut flour or almond flour in this recipe. I haven’t tried this recipe with whole wheat flour but I think it would work!
- Sweetener: You can sub maple syrup for the honey in this recipe.
- Add ins: I like adding chocolate chips. Chopped nuts, dried cranberries, or seeds are also delicious.
- Spices: You can use 3.5 teaspoons of pumpkin pie spice in these muffins. If you do not have nutmeg or cloves, just add a little bit more cinnamon/ginger.
Overall, these are great for healthy pumpkin muffins. I will say, when I tried them fresh from the oven, nice and warm, they were extremely bland unless I got a bite with a chocolate chip. I was about to write them off but decided to try one cold. YUM. For some reason the pumpkin and spice flavor pops much more cold. Ultimately, I will make again!
Can I use 3 eggs instead of 2 and an egg white?
I don’t think that would work, sorry! If you have 3 eggs… just use 2 of them, and use the whites per the recipe 🙂
Ever since I made these for the first time, I have made them every Sunday for the week for the past month!
So glad you liked them, Ramsie! Thank you so much!
Just made these and they are so good! Super moist and flavorful. Like Fall in a bite 😉
Glad you like them, Kelly! Thank you so much!
Do you know macros I’d you cut out sugar and uses stevia?
No I don’t but you can put the recipe into My Fitness Pal. I wouldn’t recommend this substitution because it will likely affect the texture of the muffins.
Love these for the healthy ingredients gluten and dairy free!! Great recipe
One question, I used Maple syrup vs honey would this make it less sweet tasting? Not looking for too sweet but my husband likes sweet even if not too sweet.
I feel like I taste baking soda ish… so thought the Maple syrup may take down sweetness which brought out the soda?
I have to say though they are great moist texture and they raised beautifully!!
Thanks!
Glad you liked them! Swapping maple syrup shouldn’t make them taste like baking soda.. I’m not sure why that would’ve happened! did you cut down the amount of maple syrup? that could’ve affected the taste.
what temp do u bake it at and how long do u bake it for?
Please read the recipe – it’s all listed. Bake at 350 for 20-25 minutes
The best soft decadent muffins there ever was. Without guilt!
thank you so much, Alex!
These are great! I altered the recipe a bit–I used maple syrup instead of honey and reduced the amount from 1/2 c to 1/4 cup. I also just used pumpkin pie spice since that is what I had on hand.
Definitely recommend!
Thank you so much, Danielle! Glad you liked it!
I love these! And so do my kids! Win, win!
Thank you so much, Becca!
I love how easy these were to make! I’m a sucker for baked goods and anything pumpkin, but I’m always looking for healthier options. I added some dark chocolate chips and it was the perfect touch. Even my picky toddler loved them! This recipe will become a fall staple.
hanks, Kaileigh! So happy you all enjoyed!
Soooo good! I’m always looking for a healthy afternoon snack for my kids and these are it! So flavorful and perfectly sweet. I made them into mini muffins and cooked them for about 11 minutes; perfection!
Thanks so much, Molly! Glad you all enjoyed them!
Holy PUMPKIN!!! These are amazing I feel so guilty lol!
Love how clean these are! Used gluten free oats and almond milk to make dairy and gluten free! Also used Lily’s chocolate chips!
I am enjoying these out by our fire with some pumpkin beer and I am in Fall heaven!
You need to try this recipe ASAP! Thank you for another amazing recipe!
So happy you enjoyed them, Cheryl! They’re the perfect fall food!
These were so delicious! Not like I ate the whole batch myself in 2 days or anything 🤤
So glad you liked them!!
We love these! I’m a huge fan of anything pumpkin and make these year round. Toddler approved too! 🙂
So glad you like them, Kieran!
First, I have to tell y’all a funny moment I got from reading your recipe. It was when I read the “Add Ins”. I read “Add ins: I like adding chocolate chips, but nuts,” Then I stopped and said “but nuts? What in the world could “but nuts” be? Where would I find “but nuts”? I’ll have to do research on them.”
But then I went on reading the sentence and realized it wasn’t “but nuts” but what it meant was that you like add chocolate chips, but (you could also add) nuts, dried cranberries, or seeds are also delicious. Well, I laughed at myself and thought y’all maybe could use a little smile or laugh.
I am anxiously waiting to make these muffins just like the recipe states and also try so many great suggestions from your readers like:
1) Arrowhead Mills Protein Powder (vanilla)
2) pepitas, flax seeds,
And some of my ideas are:
1) I have a mixture ofx, hemp & chia seeds that I buy and would love to add to recipe.
2) Apple sauce, possible replacement? or addition to? I remember reading about replacing oil in cake, muffin mixes with applesauce. I am thinking about the unsweetened chunky applesauce.
3) Raisins
4) Walnuts
5) I’d like to find a replacement sweetener for the honey, maple syrup which would not raise my blood sugar level. I am wondering if I could use Swerve Brown Sugar sweetener along with the applesauce. I definitely think adding the Swerve Brown Sugar and maybe mixed with chopped walnuts and put that on top of the muffins.
6) I need to research baking soda and if there are any healthy low salt replacements for that.
My concerns in recipes are gluten free, low salt, sugar-free & low on the glycemic index, high protein, low carb, very-low cholesterol, low calories. But if the ingredients are very healthy then a compromise with calories and carbs (to an extent).
Well, I hope this makes sense to someone and at least make y’all smile!!!
May I make a suggestion to your website guru? Could they please, please, change the icons for facebook, twitter, pinterest Yum, and email to either the right side of the screen or be moveable by us to get it out of the way of reading. It is on the left and all text is left aligned so it interferes with reading. I keep having to scroll up and down to read anything.
Hi Pat – I really can’t offer any advice here. This recipe is gluten free, refined sugar free. It is NOT: completely sugar free, low on the glycemic index, high protein, low carb or a low calorie food. So I don’t think that it is the recipe for you. Walnuts, hemp seeds and flax seeds are all high in calories, so that will just make this a higher calorie muffin. Raisins are very high in sugar and high glycemic index. If you’re going to substitute applesauce for oil you should use smooth applesauce as the chunks can alter the texture of baked goods. We try to provide as many substitutions as possible, but you’re wanting to basically make an entirely different recipe. I’m pretty confident that making these substitutions will result in a mushy, dense muffin, and if you omit the baking soda it will definitely not rise. I wish I could offer more help – but you might want to research keto recipes and see if those are a better fit as they’re often lower carb and sugar free. This doesn’t seem like the recipe for you!
These are delicious – have made them a few times! Will be making again soon!
Can I use coconut milk?
Yes you can! Please read the substitutions section: Milk: You can use any milk you like in this recipe. Dairy or non dairy (almond, soy, oat, coconut) will all work
Love anything pumpkin.. these were awesome!!
Thank you so much 🙂
do you think I could sub regular maple syrup for the honey?
Hi Misty – I’m sorry but I haven’t tried that. I think it would work but healthy baking is so finicky I can’t be sure without testing it.
Someone made a comment about whole wheat flour. I did not see that ingredient in these muffins?
There is no whole wheat flour in this recipe. I can’t be sure how it will turn out if you use that instead.
I already can’t wait to make these again! I skipped the chocolate and had these for breakfast.
Yay! Love to hear that, Kate!
I tried and found it very tasty. I made it with banana too. The batter with banana version was rather wet or more liquid like but the muffins still came out fine. Yet, it has too much sodium for my daily diet. Any suggestions to work around this? Thanks.
Hi Tam – Glad you liked it. We also have a recipe that you might like. The sodium in this comes from baking powder and you can’t make the muffins without that. The average recommended daily sodium intake is roughly 2300mg per person… and these have about 200mg per muffin. That’s less than 8% of your daily value. Maybe try to find a muffin without baking soda? I don’t think you will be able to find a pumpkin muffin with less sodium though.. most muffins have butter and milk which both add sodium
If I use gluten free flour in place of the old fashioned oats, will the pumpkins come out okay?
Hi Sylva – I can’t guarantee that will work because I’ve never tried it. I would use gluten free oats instead!
Hi, I am so glad to have found your website. I see a lot of things I want to try. I made your zucchini and banana breads and loved them both. Can I use quick cooking oats to make the oat flour for this recipe??
Hi Jamie – You can use quick cook oats in place of old fashioned oats. Steel cut oats will not work.
Absolutely delicious! These will not last long! I love anything and everything pumpkin! Can’t wait to try the pumpkin bars!
Thank you so much, Melissa! I appreciate it!