These Healthy Pumpkin Muffins are one of my go-to snacks to bake during fall. My recipe uses an entire can of pumpkin (no leftovers!) and will make your home smell amazing! The muffins are incredibly easy to make, and they turn out so moist (while being 100% whole wheat!)
One of my favorite fall bakes!
My family loves to cozy up for fall with allll the spiced pumpkin treats – and these healthy pumpkin muffins make me feel a little better when there’s been an endless stream of Chocolate Chip Pumpkin Cookies, Pecan Streusel Pumpkin Bread and Pumpkin Cinnamon Rolls running through our house.
I usually do reserve the very sweet treats for the weekend, but I always need quick snacks for the kids during the week. Baking healthier muffins is one of my favorite ways to have something in the fridge at all times, they are so easy to make and so portable – perfect to grab and go.
This recipe is incredibly easy – whisk the wet, incorporate the dry, and bake. You can make the optional little oat streusel if you want to make them feel a little more special, but they taste amazing plain as well.
I really wanted to create a recipe that uses an entire can of pumpkin (nothing worse than that half-empty can you inevitably end up throwing out most of the time!), so I was anxious to see if it works with a whole 15 ounces of puree in the muffins. But my fears were without reason – it works amazingly well and the pumpkin flavor really comes through that way!
Ingredients I like to use (plus notes)
Here is a visual overview of the ingredients in the recipe. Scroll down to the printable recipe card at the bottom of this post for quantities!
- Pumpkin: Libby’s is my go-to brand for canned pumpkin, but I do make my own pumpkin purée a lot as well. It’s so easy and so much cheaper – just cut up a pumpkin, roast it until tender and then blend until smooth!
- Flour: Feel free to use all-purpose flour if you don’t like whole wheat (although you can’t really taste or see it in these muffins). Half white, half whole wheat or white whole wheat also work.
- Corn starch: This is to keep the muffins fluffier. It’s entirely optional, just use another 2 tablespoons flour instead if you want to skip it.
- Brown sugar: This is optional if you want a sweeter muffin. Without the sugar, they are very moderately sweet. I have made them both with and without the brown sugar and they taste amazing either way. They are sweeter with the brown sugar (so more like a healthier treat), but if that’s what you’re going for and you don’t mind a little sugar then definitely make them this way (they taste SO decadent!).
- Pumpkin spice: If you’re not a fan of intense pumpkin spice flavors, use half cinnamon, half pumpkin spice.
- Optional topping: This is completely optional, just makes them a little extra-special.
How to make healthy pumpkin muffins
Just a heads-up before you start: We finished off the entire first batch within 24 hours, so I suggest you at least double it if you plan on freezing any. Really – they are SO good!
Now let’s walk through the recipe quickly, and I’ll share any tips I have to make sure your pumpkin muffins turn out perfectly the first time you bake them!
Kitchen notes/baking tips
- Baking temperature: Normally, I bake muffins at a high temperature for the first 5 minutes. But with the large quantity of honey in these, we use a lower baking temp throughout. So the 330°F for preheating is correct! These muffins bake at a slightly lower temperature so the honey in them doesn’t burn and turn bitter.
- Muffin liners: When it comes to healthy muffins, they tend to really stick to the liners a lot of the time. The only muffin liners I’ve found that comes off easily every single time are the recycled liners from If You Care – they’re amazing, and I never use any others now! You can buy them here on Amazon (this is an affiliate link and I earn a commission for purchases made after clicking through).
- Muffin batter: You can make these the classic way – mix wet and dry separately first, then combine. You can also make them as one bowl muffins: Whisk all the wet, then whisk in the spices and leavenings very well, then fold in the flour. I almost always make muffins using this one bowl method now.
- Overmixing: The most important thing in this recipe is to NOT overmix the flour – especially important with whole wheat and the high pumpkin quantity. We do not want to develop the gluten, or the muffins may become dense and gummy.
- Batter distribution: The easiest way to get the batter to muffin cups is a large cookie/ice-cream scoop with a trigger release. I’ve been doing this for almost 15 years now. If you don’t have a large cookie scoop, use two tablespoons – one to scoop up the batter and the second to scrape it into the muffin cup.
- Optional topping: If you want to add the optional streusel topping, do so right before baking – it’s just oats, pecans and pumpkin spice crumbled together with a little butter. If you’re feeling fancy, you can add some brown sugar, too. Or alternatively, push a few pepitas into the top of each muffin!
- Baking time: The muffins need around 25 minutes to bake in my oven, due to the lower baking temperature. Be sure to start checking them after 20-22 minutes, so they don’t end up overbaked.
Freezer tips
These are easy to freeze! Just add them to a freezer-friendly bag or container once they’re completely cooled. Label the bag with the name and use-by date (freeze for up to 3 months) and stick in the freezer.
To defrost, remove from the container and place the muffins on a rack on the kitchen counter (this is to prevent sogginess from thawing) for a few hours. You can warm them in the microwave or oven if you like.
The Best Healthy Pumpkin Muffins
Ingredients
Dry Ingredients
- 1 ⅓ cups whole wheat flour (spooned and leveled)
- ¼ cup brown sugar (optional)
- 2 tablespoons cornstarch
- 1 tablespoon pumpkin pie spice
- 1 teaspoon baking powder
- ¼ teaspoon baking soda
- ¼ teaspoon salt
Wet Ingredients
- 2 large eggs
- 1 (15-oz) can pumpkin
- ½ cup runny honey
- 1 teaspoon vanilla extract
Instructions
- Prep: Preheat your oven to 330°F. Line a 12 cup muffin tin with nonstick muffin liners.
- Combine ingredients separately: Whisk together all dry ingredients in a large bowl. In a separate measuring jug, whisk together all wet ingredients.1 ⅓ cups whole wheat flour, ¼ cup brown sugar, 2 tablespoons cornstarch, 1 tablespoon pumpkin pie spice, 1 teaspoon baking powder, ¼ teaspoon baking soda, ¼ teaspoon salt
- Make the batter: Pour the wet ingredients into the bowl with the dry ingredients. Fold just until combined, do not overmix. The batter will be quite thick.2 large eggs, 1 (15-oz) can pumpkin, ½ cup runny honey, 1 teaspoon vanilla extract
- Add to muffin pan: Evenly distribute the muffin batter between the prepared muffin cups (I find it works out the neatest if I do this with a large cookie scoop). Add streusel, if desired.
- Bake the muffins: Bake in the preheated oven for 23-25 minutes, or until a toothpick inserted into the middle of a muffin comes out just clean.
Notes
More healthier baking
- Healthy Banana Bread
- Zucchini Bread Breakfast Cookies
- Cinnamon Apple Baked Oatmeal
- Zucchini Oatmeal Muffins
Lorena says
Can you use gluten free flour?
Nora says
Hey Lorena, you can definitely give this a try with gluten-free flour, but I can’t fully guarantee the results since gluten-free baking can be a bit unpredictable sometimes! A good all-purpose gluten-free flour blend made for baking is your best bet — it’ll give you the closest texture to regular flour.
If your blend doesn’t have xanthan gum or a similar binder, adding a pinch could help hold everything together. Just swap it one-for-one with the regular flour and see how it goes!
Let me know if you try it — I’d love to hear how they turn out! 🧡🍁🧁
Kelsey says
love this recipe! I adjusted the recipe a bit. swapped the whole wheat flour for keto King Arthur flour. Also added a dash of maple syrup. only used a bit of honey. swapped half the brown sugar for swerve. I absolutely love how these turn out! I’ve made them twice. they are fluffy and taste like a pumpkin pie! I love eating them with chai tea in the morning!
Marcie says
I have never heard of adding cornstarch to muffins. What is the purpose of this? It doesn’t seem like a healthy ingredient
Nora says
It makes them a little fluffier, the 100% whole wheat tends to yield a very dense crumb and the cornstarch lightens this a little. I believe it’s a justified trade-off to make the wholegrain muffins a little tastier with such a small amount of cornstarch, but you can skip it and just add another tablespoon of flour instead if you prefer.
Sarah says
I have made these 3 times now . I use roasted buttercup squash mashed instead of pumpkin . Topped with a bit of cinnamon sugar . My 5 year old grandson loves these as well as the adults . Thanks for the great recipe .
Marilyn Hughesj69 says
So moist! Followed the exact recipe and they turned out perfectly! Thank you!
Terry says
Is the pumpkin purée or pie filling. I used purée and they are not the best tasting.
Nora says
Pure pumpkin, not pie filling. Sorry you didn’t like the taste, Terry. They are supposed to be healthy, so they definitely aren’t going to taste like indulgent, cake-like muffins.
Mary Ann says
I found the muffin stuck to the paper cup.
Nora says
Mary Ann, I use nonstick liners so I never experienced the muffins sticking. If your muffin cups aren’t non-stick, it is usually recommended by the manufacturer to spray them with non-stick cooking spray. Also, if you tried to remove the muffins while warm, it’s much harder to get them out. They usually release much more easily once completely cooled (at least in my experience). Hope this helps!
Adrienne says
What can I use instead of cornstarch?
Nora says
Adrienne, you could just use some plain flour instead. Hope this helps!
Fui says
Can I replaced the can pumpkin with fresh mashed pumpkin? If so, should I followed The recipe of 115oz? Thank you!
Nora says
Yes, you can! I recommend blotting freshly mashed pumpkin puree dry with paper towels to make sure it isn’t too watery. Sorry for the confusion about the amount, there are parentheses missing. It is 15 ounces of mashed pumpkin, or 2 cups. Hope this helps!
Gracie says
I made these with half ap flour and half oat flour, left out the brown sugar, and added some mini chocolate chips and chopped pecans… oh boy. So good. Thank you so much for the recipe! 🙂
Cassie says
These pumpkin muffins are my new favorite! I was a little skeptical with no oil and 100% whole wheat flour, but my family loved them! I love that there is SO much pumpkin in these muffins and that they’re made with good ingredients. I didn’t have any nuts for the topping, but will definitely make these again with the topping.
I made these into 42 mini muffins, perfect for a sweet little snack, and great for packing in my sons lunches.
Donna says
These pumpkin muffins were amazing. I added some mini chocolate chips, yummy!! I used foil cupcake liners. They worked perfectly!
MaryAnn says
They were delicious! Even without the brown sugar or the topping! Tho I would like to try it with the topping next time!! Thanks!!
Roberta Salas says
These muffins were amazing! Moist and very tasty. Will be my go to pumpkin spice muffins from now on.
Katie says
Omg! These were so good, I made a few adjustments as I didn’t have all pumpkin, added 1/2 cup applesauce, and then also some wheat bran, some toasted walnuts and craisins….unbelievable!
Nora Rusev says
Love your modifications, Katie! Thanks for sharing – I appreciate your time!
Laura says
Definitely moist ! I think I added a bit too much salt – will make recipe again ! Thx
Nora says
I’m so glad to hear this, Laura! Hope you’ll like them even better with a little less salt.
Becca says
I made these and they’re great! But the muffin papers got stuck on them and I lost the bottoms on all my muffins! Any advice?
Nora says
Becca, healthy muffins tend to stick to muffin liners more than regular muffins. What muffin liners are you using? Are they nonstick? If they’re just regular paper cups, I recommend spraying them with cooking spray. Also, make sure you let the muffins cool completely before removing the liner, that helps too. I don’t know if you saw which liners I recommend in the post, but go check it out – it’s the If You Care muffin liners. They’re a little more pricey, but they are the only liners I have never had a single muffin stick to.
Brittany says
Hi! I can you tell me where you’re located? I’m in Colorado and often have to adjust baking recipes for altitude depending on where they originate. Thanks!
Nora says
Hi Brittany, my altitude is about 2000ft! Hope that helps.
Kym says
Made these this am. Very good. Moist. I used 1/2 honey 1/2 unsweetened applesauce. Added stevia sugar to sweeten. Raised nicely?. Topped with oatmeal and cinnamon
Made 12
Julie says
I’m in Australia and have never seen pumpkin spice in the supermarket. Just wondering what spices it contains so I can do my best to replicate?
Nora says
Hi Julie, 50% cinnamon, 25% ground ginger, some ground cloves and some ground nutmeg! Hope that helps 🙂
Mary says
Beat pumpkin muffins ever! I couldn’t find the recipe I used last year so I found these on Pinterest – so happy! They’re perfect!!
Nora says
I’m glad you found the recipe, Mary! They’re one of my favorite fall treats 🙂
Shelley says
Awesome recipe loved the miffins
Nora says
Glad to hear it, Shelley!
Amy says
My freezer is stocked with these for beach to school ! They turned out so well, thank u!
Nora says
That’s so great, Amy! I already made zucchini bread and banana bread for the freezer, but now I’m thinking I need to add some pumpkin muffins, too!
Cheryl says
made these with the kids on a rainy day with a leftover can of pumpkin I found in the pantry and we’re a total hit! Thanks for the recipe. Will definitely make again
Nora says
Glad to hear the muffins were a hit, Cheryl! I love baking with my kids, so I’m happy you enjoyed making these with yours. Thank you for coming back to leave a review – I appreciate it!