Grab that cinnamon and ready the can opener. It’s time to bust out the pumpkin! Supremely moist, naturally sweetened, and packed with pure pumpkin flavor, I perfected this Healthy Pumpkin Muffins recipe over four separate attempts just for you and your fall fervor.

Healthy pumpkin muffins in a muffin pan

When I posted these Healthy Pumpkin Cookies last week, I was hesitant to fully embrace pumpkin season and the thicker sweaters that come with it.

Buuuuut after I shopped ransacked Trader Joe’s, where the festive fall foods were out in full form (check my Instagram “Favorites” highlight for the haul), I went from pumpkin prudent to pumpkin palooza.

Fall baking, here we come!

These tender muffins are sweetened naturally with honey or maple syrup.

I also added oats for their homey flavor and subtle texture.

Since pumpkin can be bland on its own, I made sure to be generous with the warm spices that are critical to bringing out its quintessential taste: cinnamon, nutmeg, ginger, and allspice ensure these muffins are bursting with fall flavor.

If you are the kind of person who lives for the smell of pumpkin spice and harvest-scented candles, you are going to adore the way your kitchen smells as they bake!

Easy healthy pumpkin muffins

In Search of the Best Healthy Pumpkin Muffins

This recipe began as an innocent adaptation of my one-bowl Healthy Pumpkin Bread.

I had been craving pumpkin oatmeal muffins so I thought, “Great! I’ll just swap out some of the flour in the pumpkin bread for oatmeal, bake the batter in a muffin pan instead, and we’ll be in breakfast heaven before I know it.”


It turns out that one of the things I adore most about baking with pumpkin—its natural moisture makes it ideal for creating healthy versions of my favorite snacks and treats—also means that nailing the right ratio of dry and wet ingredients isn’t, well, cut-and-dried.

All-in-all, it took me four attempts to get these muffins just right (I thought I had it after the third, then did one more tweak for verification purposes).

It was worth it!

Combine the benefits of pumpkin itself (see more in “Healthy Baking with Pumpkin” below) with the fact that these muffins are 100% whole grain and naturally sweetened with honey, and you have a wholesome recipe for fluffy muffins that you can feel good enjoying regularly for healthy breakfasts and snacks.

Healthy pumpkin muffins on a blue plate

Healthy Baking with Pumpkin

When you choose your ingredients thoughtfully, pumpkin muffins are one of the healthiest types of muffins to bake.

  • Canned pumpkin is packed with fiber, potassium, iron, and Vitamin A (which is important for boosting your immune system), as well as a number of healthy antioxidants. You can read about the additional benefits of pumpkin here.
  • Since pumpkin is so moist, it can stand in for oil and butter used in many recipes (pumpkin is a common healthy baking substitute for oil and eggs). In fact, this recipe only requires two tablespoons of oil. This helps lessen the overall calories.
  • Pumpkin’s flavor is not overwhelming, so it allows the recipe’s other flavors to shine. You can get away with a lesser amount of honey or maple syrup to naturally sweeten these muffins. (This Pumpkin Banana Bread is another of my favorite recipes that leverages natural sweetness).

PSSST!!! If you love healthy baking, I promise it’s worth getting a copy of The Well Plated Cookbook, which has muffins and many other healthy baked goods inside!

How to Make Healthy Pumpkin Muffins from Scratch

At their heart, these healthy pumpkin muffins with yogurt are meant to be a healthy breakfast item or snack.

That way you don’t have to feel guilty devouring a healthy pumpkin oatmeal muffin mid-afternoon. (Though if you are looking for a sweeter pumpkin recipe to serve as dessert, try my one-bowl Pumpkin Sheet Cake with Greek Yogurt Cream Cheese Frosting.)

This recipe is incredibly easy if you’re tight on time or don’t want to make a messy kitchen. All of the batter whips up in one bowl with a spatula (which was a major blessing throughout all of my recipe testing!).

The Ingredients

  • Pumpkin. Fall happiness + plenty of health (see above). This recipe calls for one whole can of pumpkin, so you don’t have to waste any amount of an opened can.
  • Greek Yogurt. Provides additional moisture and creates a fluffy, exceptionally moist muffin—not the typical dense muffin that can result from using 100% whole grain.
  • Oatmeal + Whole Wheat Flour. Wholesome, fiber-packed additions that give these muffins a delightfully nutty flavor.
  • Honey. To keep these muffins free from refined sugar, I sweetened them with honey (maple syrup would also work beautifully here). The honey tastes wonderful with the spices, oats, and pumpkin too.
  • Spices. Cinnamon, nutmeg, ginger, and allspice make these muffins instantly warm and cozy. They’re essential for bringing out the perfect pumpkin flavor.

The Directions

Wet ingredients in a mixing bowl
  1. Whisk the oil, honey, and yogurt together, then add the egg and vanilla.
    Pumpkin being whisked into wet ingredients
  2. Whisk in the pumpkin.
    Spices being whisked into wet ingredients
  3. Stir in the baking soda and spices.
    Muffin batter in a mixing bowl
  4. Add the flour and oats, stirring until fully incorporated.
    Batter in a muffin pan with oats
  5. Transfer the batter to the muffin pan, and top the muffins with oats for a little festive decoration.
  6. Bake the pumpkin muffins for 24 to 29 minutes at 325 degrees F. Let cool, then ENJOY!

Healthy Pumpkin Recipe Adaptations

If you’ve made Well Plated recipes before, you’ll likely know one of my go-to healthy swaps is often using applesauce in place of butter and oil.

Here, however, I do not recommend making healthy pumpkin muffins with applesauce in place of the oil. The pumpkin already contributes scrumptious moisture, so adding applesauce in addition to the pumpkin and Greek yogurt would most likely make the muffins too mushy.

These are tried and true recipe adaptations you can enjoy instead:

  • Gluten Free. Baking pumpkin muffins with almond flour is an excellent option to make healthy pumpkin muffins gluten free. Check out this recipe Almond Flour Pumpkin Muffins. You also can follow this recipe, but swap in a 1:1 baking blend for the wheat flour.
  • Vegan. My Vegan Pumpkin Muffins are a perfect fit for what you’re craving!
  • Chocolate Chips. To make healthy pumpkin muffins with chocolate chips, add 2/3 cup of your favorite chocolate chips to the batter. Or for a similar taste and texture with oats too, you’ll devour this Healthy Pumpkin Chocolate Chip Bread.

Storage Tips

  • To Store. Since these healthy pumpkin muffins are so moist, I recommend storing them in the refrigerator in a paper towel-lined airtight storage container for up to 4 days. The pumpkin flavor becomes even more pronounced on day 2.
  • To Freeze. Freeze muffins in an airtight freezer-safe storage container for up to 3 months. Thaw and enjoy as desired (I like to individually wrap my muffins so I can grab them for quick breakfasts and snacks).
Healthy pumpkin muffins with oats on top

More Healthy Ways to Bake with Pumpkin

Recommended Tools to Make this Recipe

  • Muffin Pan. With this tool, you can whip up any of my healthy muffins at any time.
  • Mixing Bowls. These are stackable and dishwasher- and microwave-safe.
  • Measuring Spoons. Perfect for recipes that require you to measure lots of spices.

Do you have a favorite healthy way to bake with pumpkin? I’m fully stocked and ready to live my best pumpkin spice kind of life!

If you try this recipe, please comment below and let me know how it turned out! I love hearing from you.

Healthy pumpkin muffins with oats on top

Healthy Pumpkin Muffins

5 from 20 votes
Easy, one-bowl healthy pumpkin muffins made with oatmeal, honey (no sugar!), yogurt, and warm fall spices. Moist, fluffy, and so delicious!

Prep: 20 mins
Cook: 25 mins
Total: 50 mins

Servings: 12 muffins


  • 2 tablespoons canola oil or melted and cooled coconut oil
  • 1/2 cup honey or pure maple syrup
  • 1/3 cup plain non-fat Greek yogurt at room temperature
  • 1 large egg at room temperature
  • 1 teaspoon pure vanilla extract
  • 1 15-ounce can pure pumpkin not pumpkin pie filling
  • 1 teaspoon baking soda
  • 1 1/2 teaspoons ground cinnamon
  • 1/4 teaspoon ground nutmeg freshly grated is an amazing upgrade! Use this zester to grate whole nutmeg.
  • 1/4 teaspoon ground ginger
  • 1/4 teaspoon ground allspice
  • 1/4 teaspoon kosher salt
  • 1 1/4 cups white whole wheat flour*
  • 3/4 cup plus 2 tablespoons, rolled oats plus additional for sprinkling on top


  • Preheat your oven to 325 degrees F. Light coat a 12-inch standard muffin tin with nonstick spray.
  • In a large mixing bowl, whisk together the oil, honey, and Greek yogurt. Once blended, whisk in the egg and vanilla. Make sure the ingredients are smooth and well blended.
  • Whisk in the pumpkin purée.
  • Sprinkle the baking soda, cinnamon, nutmeg, ginger, allspice, and salt over the top. Whisk or use a rubber spatula to stir gently to combine.
  • Sprinkle the flour and oats over the top, then with a rubber spatula, gently incorporate, just until the flour disappears.
  • Scoop the batter into the prepared muffin cups, dividing it evenly (I like to use a batter or ice cream scoop for this). The cups will be very full. If desired, sprinkle on a few oats on top for decoration.
  • Bake for 24 to 29 minutes, or until a toothpick inserted in the center of a muffin comes out clean. Super moist breads like pumpkin bread can be hard to gauge; to be 100% certain, use an instant read thermometer. The center of a muffin should register 200 degrees F. Place the pan on a wire rack and let cool in the pan for 5 minutes, then with a butter knife, gently loosen the muffins and transfer them to the rack to finishing cooling (or for as long as you can resist devouring them). The muffins will be very delicate while still warm, but will firm up more as they cool.


  • TO STORE: Since these healthy pumpkin muffins are so moist, I recommend storing them in the refrigerator in a paper towel-lined airtight storage container for up to 4 days. The pumpkin flavor becomes even more pronounced on day 2.
  • TO FREEZE: Freeze muffins in an airtight freezer-safe storage container for up to 3 months. Thaw and enjoy as desired (I like to individually wrap my muffins so I can grab them for quick breakfasts and snacks).  
  • *For the white whole wheat flour, you can substitute whole wheat pastry flour, all-purpose flour, or a blend of the two. Regular whole wheat flour can also be used, though the muffins will have a heavier texture and more pronounced wheat taste.


Serving: 1(of 12)Calories: 147kcalCarbohydrates: 27gProtein: 4gFat: 3gSaturated Fat: 1gCholesterol: 14mgPotassium: 125mgFiber: 3gSugar: 13gVitamin A: 5535IUVitamin C: 2mgCalcium: 32mgIron: 1mg

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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  1. Hi Erin,

    The muffins smell good! However, the baking time for mine seems to be doubled and it’s not done yet as I am typing now. I use the regular 12 muffin tin. I am now worried that I might over bake the outside and the inside is still kind of doughy. Thank you for your recipe!!!

  2. HI! This recipe looks so yummy. Has anyone tried subbing oat flour for the flour. Would love to make these gluten free.
    Thank so much!

    1. Hi Jeannette! Unfortunately, I don’t recommend that swap here, as regular flour behaves very differently in baking than oat flour. You could try using a 1:1 GF baking flour blend instead. I hope this helps!

  3. I love this recipe! Working on making healthier foods since we are now seniors with heart disease.. I did use whole wheat flour by accident thinking that’s what it said haha, turned out great but, a little more bland to my liking, so next time I will try adding more on the spices. The texture is wonderful and the honey was just enough sweetener. Can’t wait to try your other recipes..5 stars

  4. These are amazing and I don’t feel guilty eating them. Seriously delicious and couldn’t wait to have one each morning. These will surely become a staple in our house. Bravo!5 stars

  5. I love these muffins SO MUCH! I halved the amount of honey and didn’t use greek yogurt. And substituted wheat flour for normal All-Purpose flour. It turned out SO delicious! I also made them in a mini muffin tin. So cute! 100% recommend you try. Note: Mine were a little doughy at first to but after a few hours they set up perfectly fine.5 stars

  6. The muffins came out perfectly! They were a tad dry but that could because it was my first time making them. I used maple syrup, added walnuts and added extra Trader Joe’s Pumpkin Spice. A perfect, healthy snack for mid-morning coffee!5 stars

  7. I wasn’t the only one in the family doing a happy dance enjoying these wonderful muffins for an anytime snack. The pumpkin, spices and oatmeal combine for a flavorful “Party” on your tastebuds! My husband declared: “You can make these often as you want, they’re sooo good!” I can’t argue with that sentiment. Thanks for another magnificent recipe that will be used often and relished every time they’re eaten! They’re so moist, easy to make and flavorful. I didn’t have a muffin tin so I used a non-stick 8×11″ pan with an 18 portion divider insert and they turned out perfect.5 stars

  8. I love these muffins! I’m a fellow foodie, and I’m always looking for healthy, yummy recipes. I really love that this recipe consists primarily of pumpkin puree, greek yogurt, oats, and maple syrup. So much healthier than other muffin recipes. I first made these with my niece and nephew. Immediate family favorite! I’ve made them again plenty of times. They are a guilt-free dessert or breakfast for me. I like to eat them with nonfat greek yogurt. Great for all seasons and any meal or snack! Thanks!5 stars

  9. Hye Erin,
    Im from Kuala Lumpur,Malaysia, Thank you sharing this recipe. Muffin smell so good & so yummy!!.I like it very much😘

  10. Really enjoy these muffins! Second time making this recipe. I love that the recipe uses a whole can of pumpkin (I always forget about leftover canned pumpkin!) I bought vanilla Greek yogurt by mistake, worked out fine. I also added a handful of chopped walnuts for crunch.

    I’m pregnant and this has been one of my favorite breakfasts!5 stars

  11. Erin, thank you for this outstanding recipe! I rarely leave comments, but I just had to acknowledge your incredible work here. I only used a dollop of yogurt, 2 teaspoons TJ’s Pumpkin Pie Spice, extra virgin olive oil, whole wheat pastry flour and added chopped walnuts like another reviewer. I appreciate that they’re not too sweet. Just finished my second one straight out of the oven :D

    In gratitude, Jean5 stars

  12. Great muffin for those trying to cut added sugar. I had a partial can of pumpkin puree and used applesauce for the remaining balance. I also used whole wheat flour. I believe the yogurt really helped produce the rich, dense, moist results.5 stars

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