These are the BEST Healthy Pumpkin Muffins on the web! This recipe uses an entire can of pumpkin (no leftovers!) and will make your home smell like autumn. These are incredibly easy to put together and they turn out so moist.
The recipe uses all whole wheat flour and using the brown sugar is optional, so you can make them naturally sweetened with only honey.
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 😉
This is a simple clean muffin made from scratch (and it’s up to you to add the yummy oatmeal streusel for an extra treat!) – the perfect fall, Halloween and Thanksgiving holiday treat.
Muffins are one of my all-time favorite breakfast and snack foods – and you’ll never find me without at least two batches of muffins in the freezer!
These wonderfully cozy Healthy Pumpkin Muffins are no exception. They’re in our regular rotation for fall and my kids start waiting for me to make them as soon as school starts back up after the summer.
Pumpkin is simply perfect to use in healthy muffins. It adds so much moisture and sweetness (read: you won’t need as much fat or sugar!) and gives the muffins a certain stability and fluffiness – even though they’re made with whole wheat flour and optionally without any refined sugar.
These Healthy Pumpkin Muffins
- can be made without any refined sugar for an extra-healthy treat
- are easy to whip up with just a handful of simple staple ingredients
- can be frozen to keep on hand for those busy days!
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.
So, these really ARE made with an ENTIRE CAN of pumpkin (so, no pesky leftovers sitting in the back of your fridge – though you could always make a batch of Pumpkin Waffles if you just so happen to be looking for a recipe to use said leftovers).
I have made many a healthy muffin in my lifetime apple cinnamon, chocolate banana, blueberry oatmeal or gingerbread to name a few), but these are by far the best I’ve ever (ever!) made.
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, you won’t believe you can feel good about tucking them into lunch boxes or using them as a quick on the go breakfast.
Read on for the detailed steps, or scroll down for how to freeze these muffins, more tips to make this recipe foolproof and the printable recipe card.
► 1 Prep: First, you’ll want to get out a bowl and a measuring jug, line a 12 cup muffin pan with muffin liners and turn on your oven to 330°F. These muffins bake at a slightly lower temperature so the honey in them doesn’t burn and turn bitter!
PSA: 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!
My favorite muffin liners are from If You Care – I never had a muffin stick to them! You can buy them here on Amazon (this is an affiliate link and I earn a commission for purchases made after clicking through).
► 2 Mix muffin ingredients separately: To make the best muffins, it’s important to first mix the dry ingredients and the wet ingredients separately. That way you can mix them together really well before they come together.
So, add all dry ingredient to a bowl and stir to combine them well (especially get that baking powder mixed in evenly!) and add all the wet ingredients to a large measuring jug and whisk them together really well until smooth and evenly colored.
► 3 Make muffin batter: Pour the wet ingredients into the bowl with the dry ingredients (this is where it comes in handy to use a measuring jug – mess-free pouring!). Use a spatula or a wooden spoon to JUST combine the wet and dry ingredients. Lumpy batter is perfectly fine! Also, the batter is quite thick from all the pumpkin, that’s fine, too.
► 4 Add muffin batter to muffin cups: Evenly distribute the batter for your healthy pumpkin muffins between your prepared muffin cups. I usually do this with a large cookie scoop because it’s fast, easy and mess-free!
I have a cookie scoop similar to this one on Amazon! (This is an affiliate link and I earn a commission for purchases made after clicking through.)
► 5 Bake the muffins: If you want to add the optional streusel topping, do so now – 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. Then bake the muffins for around 25 minutes, or until a toothpick inserted into the middle comes out just clean.
Tips for the Best Ever Healthy Pumpkin Muffins:
- Do not overmix this batter!
Due to the high quantity of pumpkin puree in this recipe (one entire 15-oz can!!) and 100% whole wheat flour, you really have to be careful not to overmix this batter.
It’s totally fine if you have a few lumps, if you mix it too much you’ll end up with dense and gummy muffins instead of fluffy goodies.
Using the cornstarch does help combating this a little, but I recommend gently folding just until you can’t see any more dry flecks of flour.
- Adjust the sweetness to your taste
I made them both with and without the brown sugar and they taste amazing either way.
They are quite sweet 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!).
If you want to avoid the sugar completely, simply leave it out for an all-honey sweetened muffin.
- Add a little something extra with the topping
I added the topping on a whim when I made these for the blog, because they look a little plain on photos without it.
Combine 3 tablespoons quick cooking oats, 1 tablespoon chopped walnuts or pecans and ½ teaspoon pumpkin pie spice in a medium bowl. Cut in 2-3 tablespoons stick butter and mix with your fingertips until small crumbs form.
Sprinkle over the muffins just before baking, slightly pressing it into the batter to help it stick.
How to Freeze Healthy Pumpkin Muffins:
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.
More Pumpkin Breakfast Recipes
And if you liked these recipes, there’s plenty more to make family meals easier for you! Be sure to join my FREE recipe circle here to get easy recipes by email.
P.S: If you tried this recipe, why not leave me a comment below to let me know how you liked it?
The Best Healthy Pumpkin Muffins
Recipe details
Equipment
- toothpick
Ingredients
Dry Ingredients
- 1 ⅓ cups whole wheat flour
- 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.
- 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.
- 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
Nutrition
More recipe information
And don’t forget adding that comment and star rating below – I can’t wait to hear what YOU think of our favorite healthy pumpkin muffins!
P.S: Want more pumpkin recipes?
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!