Healthy Pumpkin Muffins
Easy, healthy pumpkin muffins made with whole grains, natural sweetener (maple syrup) and real pumpkin! These muffins are fluffy and delicious.
Updated by Kathryne Taylor on August 30, 2024
We caught our first cool fall breeze this week. Do you know what that means? It’s pumpkin muffin time.
I snapped some new photos of my favorite pumpkin muffin recipe as I satisfied my pumpkin craving. These pumpkin muffins are perfect for chilly fall mornings and afternoon snacks.
They’re healthier than most, since they’re made with whole wheat flour and oats, sweetened with real maple syrup or honey, and call for coconut oil or olive oil instead of butter. Believe it or not, this healthy pumpkin muffin recipe yields light and fluffy muffins.
These pumpkin muffins wouldn’t be complete without plenty of warming spices, including cinnamon, ginger and nutmeg. Most “pumpkin spice” flavor comes from the spice, not the pumpkin!
I love these muffins with a spread of almond butter, peanut butter or pecan butter on top. Nut butter adds some extra protein, which means that I’m not hungry before lunchtime. If you’re going pumpkin-crazy this time of year, enjoy your muffin with a homemade pumpkin chai latte.
These pumpkin treats have the magical power to convert “healthy muffin” skeptics into fans. Let’s make some!
The Best Pumpkin Muffins
Five reasons to love this pumpkin muffin recipe:
- These muffins are easy to make with basic ingredients. Only one bowl required!
- They’re made with 100% whole grains, yet they’re fluffy and delicious. No one will know the difference.
- They’re also naturally sweetened with maple syrup or honey, rather than loaded with refined sugar. The maple syrup (or honey) offers a touch of extra flavor, which I love.
- These muffins feature a few of your favorite warming spices so they taste like your favorite pumpkin latte.
- They freeze well for later, too. Just defrost individual muffins in the microwave for 30 to 60 seconds, or until gently warmed through. You don’t want to overdo it.
Healthy Pumpkin Muffin Notes & Tips
Change it up. Add nuts, chocolate chips or chopped fruit cranberries or crystallized ginger. See recipe notes for details.
Simplify the recipe. Substitute 2 teaspoons store-bought pumpkin spice blend for the individual spices (cinnamon, ginger, nutmeg and allspice). Or, if your spice drawer is empty, simply use 1 1/2 teaspoons ground cinnamon and call it good.
Craving a sweet topping? Liz topped these muffins with my maple glaze from my pumpkin scones recipe, which sounds marvelous.
This muffin recipe is special diet-friendly. You can easily adjust this recipe to make it vegan, dairy free, egg free and/or gluten free. See the recipe notes for details.
Watch How to Make Healthy Pumpkin Muffins
Baking Tips for Success
How to Measure Flour
How you measure your flour is important. Why? If you measure incorrectly, you could end up with up to 50 percent extra flour, which will make your muffins dense, dry and flavorless. Use the spoon and swoop method:
- Gently stir your flour to loosen any clumps.
- Spoon your flour into the measuring cup with a big spoon or a flour scoop. Do not scoop up the flour directly into the measuring cup.
- Level off the top of the cup with a knife. Repeat as necessary.
Use Baking Soda, Not Baking Powder
They are not the same thing. Both are leaveners that help your baked goods rise (baking powder contains some baking soda, but that’s a long story). For ideal results, always follow the recipe and measure carefully.
How to Stir Your Batter
This muffin batter is super simple to stir together by hand, and that’s how I recommend making these muffins. Why? Whipping your batter will make the flour’s gluten protein too strong, yielding tough muffins.
I know it can be tempting to use a stand mixer or hand mixer when it’s within reach. Please don’t! Follow the instructions below and you’ll end up with light, fluffy muffins.
More Pumpkin Treats & Fall Muffins
Craving more? You’re going to love these recipes:
- Healthy Pumpkin Bread (like these muffins, but in bread form)
- Pumpkin Pecan Scones with Maple Glaze
- Pumpkin Pancakes
- Perfect Roasted Pumpkin Seeds
- Healthy Banana Muffins
- Healthy Apple Muffins
Please let me know how these pumpkin muffins turn out for you in the comments. I love hearing from you, and hope these pumpkin muffins become your new favorite.
P.s. That beautiful mug in the photos above and below? That’s handmade by my friend Margaret.
Healthy Pumpkin Muffins
Easy, one bowl, healthier pumpkin muffins made with whole wheat grains and naturally sweetened! These pumpkin muffins are as light, fluffy and delicious as their coffee shop counterparts. Recipe yields 12 muffins.
Ingredients
- ⅓ cup melted coconut oil or extra-virgin olive oil*
- ½ cup maple syrup or honey
- 2 eggs, at room temperature
- 1 cup pumpkin purée
- ¼ cup milk of choice (I used almond milk)
- 2 teaspoons pumpkin spice blend (or 1 teaspoon ground cinnamon, ½ teaspoon ground ginger, ¼ teaspoon ground nutmeg, and ¼ teaspoon ground allspice or cloves)
- 1 teaspoon baking soda
- 1 teaspoon vanilla extract
- ½ teaspoon salt
- 1 ¾ cups whole wheat flour**
- ⅓ cup old-fashioned oats, plus more for sprinkling on top
- Optional: 2 teaspoons turbinado (raw) sugar for a sweet crunch
Instructions
- Preheat oven to 325 degrees Fahrenheit (165 degrees Celsius). If necessary, grease all 12 cups of your muffin tin with butter or non-stick cooking spray (my pan is non-stick and didn’t require any grease).
- In a large bowl, beat the oil and maple syrup or honey together with a whisk. Add the eggs, and beat well. Add the pumpkin purée, milk, pumpkin spice blend, baking soda, vanilla extract and salt.
- Add the flour and oats to the bowl and mix with a large spoon, just until combined (a few lumps are ok). If you’d like to add any additional mix-ins***, like nuts, chocolate or dried fruit, fold them in now.
- Divide the batter evenly between the muffin cups. Sprinkle the tops of the muffins with about a tablespoon of oats, followed by a light sprinkle of raw sugar and/or pumpkin spice blend if you’d like. Bake muffins for 22 to 25 minutes, or until a toothpick inserted into a muffin comes out clean.
- Place the muffin tin on a cooling rack to cool. These muffins are delicate until they cool down. You might need to run a butter knife along the outer edge of the muffins to loosen them from the pan.
- These muffins taste even better after they have rested for a couple of hours! They’ll keep at room temperature for up to 2 days, or in the refrigerator for up to 4 days. They keep well in the freezer in a freezer-safe bag for up to 3 months (just defrost individual muffins as needed).
Notes
Recipe adapted from my healthy pumpkin bread.
*Oil options: I love coconut oil here. I used unrefined coconut oil and can hardly taste it in the final product. Olive oil might lend an herbal note to the muffins, if you’re into that (I tested with California Olive Ranch’s “Everyday” variety and couldn’t even taste it). Vegetable oil has a neutral flavor but the average vegetable/canola oil is highly processed, so I recommend using cold-pressed sunflower oil or grapeseed oil if possible.
**Flour alternatives: White whole wheat flour works great, if you can find it. Whole wheat pastry flour yields extra light and fluffy muffins that are delicate until cooled. All-purpose flour and gluten-free all-purpose flour blends work as well.
**Change it up: You could really go crazy with add-ins here. After stirring in the flour and oats, gently fold in up to ¾ cup chocolate chips, chopped nuts like pecans or walnuts, and/or some chopped dried cranberries or crystallized ginger.
Serving suggestions: These muffins are great on their own, with a pat of butter, or spread with almond butter. They would also be fantastic with homemade pecan butter or coconut butter.
Make it egg free: Readers report that these muffins turn out well with flax eggs!
Make it vegan: Use maple syrup, flax eggs and non-dairy milk.
Make it dairy free: Simply use your non-dairy milk of choice.
Make it gluten free: Bob’s Red Mill gluten-free all-purpose blend works well instead of the whole wheat flour. You could use 2 ½ cups certified gluten-free oat flour instead or follow my recipe for almond flour-based pumpkin muffins.
Make it oat free: Simply omit the oats. No other changes necessary.
Make it lower in fat: I would argue that this bread contains a healthy amount of fat, but you can replace the oil with applesauce if you’re following a low-fat diet. Choosing olive oil instead of coconut oil will reduce the saturated fat content; total fat content will remain the same.
Update September 24, 2019: I removed white whole wheat flour as an option simply because I can’t find it in stores any more. I also upped the amount of spice from 1 ½ teaspoons to 2 teaspoons.
Nutrition
The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice. See our full nutrition disclosure here.
Your recipes are a hit in our home, as always I made pumpkin puree and knew I had to bake some muffins! I used all purpose flour and added raisins and they turned out so good! A great recipe to make with a toddler, too.
Agreed I just made these with my 2 year old !!! So good.
Can I use Avocado Oil? What if any type of taste will the oil add?
You can try it. I haven’t tried it so I can’t say for sure, but I believe others have tried it and didn’t mind the results.
This is one of my go-to fall recipes I make every year!
Do you think it would work to replace part of the whole wheat flour for almond flour?
Thanks!
Gluten-Free Pumpkin Muffins Try these!
It’s Thanksgiving today so I took fresh cranberries and cooked them till they popped, then put a spoonful of cranberries & a little coconut sugar in the middle of each muffin. Delicious!!
Thank you for another fabulous recipe!
You’re welcome, Eliane! Thank you for your review.
Taste strongly of baking soda. I double checked I used the right amount. I think it’s because there is very little acid in the recipe to activate it?
I’m sorry to hear that. I have made these several times and didn’t have that result.
What size can of pumpkin? They are larger in Canada I think. Thank you
A can is roughly 15 oz I believe.
This recipe is wonderful! The muffins are light and reminiscent of your healthy banana muffins. So good! Is there a way to incorporate bran into the recipe to increase the dietary fiber?
Love this recipe and have made it several times. I love it with chocolate chips, or candied ginger for a little tang.
One thing I do is use the separate spices, instead of commercial pumpkin spice mix. I like to add the spices to the purée, separately, and mix them in, well. Then I add it to the rest of the ingredients. It seems to give the muffins a bit more flavor. I do the same when making pumpkin pie. Delish.
Despite the rave reviews, this didn’t work for me. Followed recipe exactly and I had a thick sticky batter that didn’t rise. Pretty disappointing.
I’m sorry to hear that. Did you add the leaveaner?
You may need to sift your whole wheat flour or substitute all-purpose flour for some of it.
I was worried about them being called “healthy” but they are delicious!!! I added chopped walnuts this time, may add dried cranberries next time.
I would love to make this Keto friendly for my diabetic friends. I can do that easily for everything except the flour. Do you know amounts of Coconut and/or Almond four. That would also make it Gluten free. Would you happen to know the exchange amounts?
Thanks, Kate!
Gluten-Free Pumpkin Muffins
Love this recipe and make it every time I have an open can of pumpkin! Would you ever consider adding weight measurements to the recipe to make it easier for those of us who prefer a scale? Thank you!
Absolutely delicious and incredibly easy to make. I made this as well as your pumpkin bread as I had an extra pumpkin to use up. I used extra virgin olive oil and used some homemade apple butter as the sweetener. Also added a good amount of mini chocolate chips.
Turned out wonderful.
That’s great to hear, Ciara!
Such a good recipe! My whole family love these muffins. Thank you for sharing.
You’re welcome, Jo! Thank you for your review.
Delicious and a five star!
Hi Kate,
Have you tried Eikorn flour of Spelt flour in this recipe? I recently bought some fresh milled flours and trying to figure out where to use the flours.
thank you
Hi Heather! I haven’t tried it for this recipe. I do know spelt flour works in my banana bread recipe.
Best pumpkin muffins ever!
How to store after baking? Do they need to go in the fridge or can they remain at room temp for a day or two? Love these!!
Either option, just use your best judgement. Thank you for your review, Jen!
I have probably made them a dozen times already. I just love them. I add chopped dates. And sometimes if I have homemade unsweetened applesauce, I use half the oil and the rest, applesauce and less maple syrup or honey. They’re absolutely amazing.
Very versatile recipe you can add and take away whatever you want and they still come out the best and stay so moist love them. Thank you for the recipe.
Not sure why this recipe call for baking soda when there is no acid ingredient to activate it. I am swapping 2-3 t of baking powder……more to follow
I made the muffins as per the recipe but added some pecans. I thought they were a bit dull on taste, though my husband liked them. They need a little spark — Perhaps some orange rind, or more ginger. A little more sweetness would be good too, perhaps with some dried fruit, or candied ginger. The suggestion of adding turbino sugar on top is a good one but not something I have on hand .
I’m sorry you didn’t love them. Let me know if you try any of your ideas! The pumpkin flavor comes from the spices so be sure to increase those and using fresh matters too. I appreciate your feedback.
Made them with puréed roasted pumpkin from my garden and they are delicious!
Thank you for sharing, Kat!
Any chance you have the measurements in weight?
I don’t, sorry!
Ive made these gluten and oat free with almond milk and maple syrup a few times now and I love them. Not only does it taste good but they’re super simple and easy to make. I’ve added pumpkin seeds on top a few times and that was fun.
These are a tremendous autumn treat! I wanted small ‘finger foods’ for a Nov. gathering, so I used small muffin cups. I added chopped crystallized ginger and walnuts (1/2 cup total) and the result was just right.
Thank you for another ideal recipe – I’m a big fan!
You’re welcome, Emkay!
Wondering what the timing may be for mini muffins?
Hi Catherine, typically you need to cut the time in half, but keep an eye on it to make sure they don’t get overdone. Let me know how they turn out!
White Wheat Flour at Kroger in Anna, IL. First time I made it using some regular WW Flour and pastry flour and they were delicious even though I did not have any topping on them!
These were a flop unfortunately – they tasted incredibly bitter like baking soda as others have mentioned below. I looked it up on Google and it recommended 1/4 tspn per cup of flour. This recipe has over double – did you perhaps mean baking powder instead of soda? Turned into chicken feed
I’m sorry to hear you didn’t love this recipe. I’ve made this recipe many times without issues.
Would this recipe work for a loaf of pumpkin bread?
I recommend my Healthy Pumpkin Bread!
How much applesauce would you use? Would you replace all of the oil or only part of it with the applesauce?
I haven’t tried it so I can’t say for sure, sorry!
Didn’t rise enough with flax eggs
Sadly lots of expensive ingredients but not great results for me. They were sunken in despite extra time in the oven. Just not enough leavening perhaps. I made them exactly per recipe but vegan with oat milk and 2 flax eggs per recipe notes for this. Wish I’d added some whipped acquafaba or baking powder versus soda or a different mix of both.
Anyway, smelled nice, just wish they had worked out.
The show nutrition button doesn’t work. How many calories per muffin?
Hi Lindsay, I’m sorry to hear that. Did you click to expand? I just checked and it looks to be working. Was the blog fully loaded? Trying to help troubleshoot.
This recipe is AMAZING! So delicious and adding in some chocolate chips just made these even better!! Definitely a new go to recipe!
Excellent recipe! And NO baking poweder:)
How can I adjust this for mini muffins?
Delicious! I found White Whole Wheat flour at our local Kroger Store in Carbondale, IL. I substitute about 1/2 cup with Whole Wheat Pastry Flour
This is a pretty solid recipe; I made this for my wife who is getting over pancreatitis and needs to eat low fat for a while. I subbed plain yogurt for the oil, used only one egg and used almond milk. They turned out just as good as their coffee shop counterparts! Nice job.
I made your Healthy Pumpkin Bread and loved it! I want to make the muffins but notice the only difference is 1/3 cup oats. Isn’t it best to use 1/3 cup less flour?
I’ve made these several times. I use a combo of white whole wheat, wheat pastry flour and oats. I add frozen cranberries and dried cranberries and pecans and cinnamon sugar on top. I tried one cup of red whole wheat but they were a bit drier. Still good. I wrap each one in plastic wrap and freeze on plastic bag. They freeze very well.
My gf version is in the oven now. I did add 1/2t baking powder. All my gf muffins call for both baking soda and baking powder. I thought it might be an oversight. If not, why not use bp?
Rating provisional since I haven’t taken them out of the oven yet, but I have been happy with most of your recipes.
I have been making batch after batch of these since the fall. I have one for breakfast with some farmer cheese as a spread, for a bit more protein. I look forward to it every single morning even though I have been having them for months! I roast butternut squash for the pumpkin.
I have made many, many of your recipes and have been using your cookbook for years. Lately, when I am looking for recipes I just turn to your web site and the NYT app, even though I have a bookshelf full of cookbooks. Thank you!!
These are sooo yummy and I don’t feel guilty eating several of them. I make mini muffins instead of full size. My toddler’s love them too. I’ve made them a few times already and add chocolate chips!
These are great! I have been making pumpkin muffins for years but these are so much healthier and just as delicious! Thanks for this great recipe!
I replaced the maple syrup with date syrup and also chopped cashews and dried dates. It turned out delicious!
Super easy and tasty muffins to make. My 8yo daughter loves them and is always requesting me to put in her lunch box as a treat. She has even converted her friend at school who hates pumpkin to luv it!! Feels good baking fresh nutritious and delicious goodies for my two younge children. Thank you!!
I make these ALL the time – everyone in our house likes them and they are my son’s all time favorite. I try to keep pumpkin and chocolate chips on hand so I can make them. They are so easy. I always make them with the flax egg option and maple syrup to keep them vegan and it works great!
I have made these muffins at least a dozen times at this point. Love them! I usually add chopped walnuts and blueberries, and sometimes mini chocolate chips.
Love, love, love this recipe so good I had to leave a review, thank you
And greetings from Melbourne, Australia.
Great recipe! I come back here again and again. Sometimes I follow it exactly – other times I change it up a bit. This time I used butternut squash puree instead of pumpkin and added raisins. Wonderful every time. Thanks for sharing your stellar culinary skills with us all!
My family loved these! Thank you!
These are really good when made with the maple syrup. It adds a lot of flavor. I used melted butter instead of oil, subbed 1/2 cup rye flour for the regular, and added chopped pecans. I also used only half the maple syrup.