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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 these (or my Pumpkin Scones) 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

4.83 from 105 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 minutes
Cook: 25 minutes
Total: 50 minutes

Servings: 12 muffins



  • Preheat your oven to 325°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°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 finish 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!

Learn more about Erin

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  1. These are very moist and delicious. I made them for the first time today. They aren’t quite sweet enough for me, so when I make them again I either will add white chocolate chips, or maybe add some regular sugar on top of the maple syrup. (they still have great ingredients, I don’t mind a little extra sugar).4 stars

  2. I’ve made this recipe several times over the past couple of years and my wife and truly like it. I can use up garden sugar pumpkin puree. I prefer to use 3/4 cup all purpose to 1/2 cup whole wheat flour for the recipe. We use honey and I like to add an extra tablespoon to the recipe to bump up the sweetness just a tad. Great healthy all-season recipe. Awesome for breakfast or as a healthy snack with cup of tea.5 stars

  3. These are amazing! For mini muffins I baked them at 325 for 15 minutes. They are the perfect snack for my preschooler!5 stars

  4. Yummy! I realized partway through that we were out of vanilla extract (how did that happen?!!). I amped up the cinnamon to 2t (would not repeat that) and zested a small orange. The orange flavor was actually delicious! It was strong enough that I rebranded them to pumpkin-orange muffins for my family. Halving or thirding the zest would probably be nice, subtle addition. This batch was a bit over-moist for me, but I may have been imprecise in some of my measures.4 stars

  5. I made these with Siggi’s coconut yogurt, used granulated honey but a bit less than called for, used coconut oil, and replaced the flour with fresh ground at home Einkorn flour, and added 72% dark chocolate chips from Trader Joe’s. These were pure heaven. Making again and again. I’ll cut back even more of the granulated honey though next time since the chocolate chips have some sugar and I don’t want them sweet.

        1. Hi Rae, Not for these muffins but you could give these a try: or these: Enjoy!

  6. I love this recipe. I use coconut cream instead of yogurt and they are moist and delicious. The only issue is that the oats dont quite cook enough and so cause a bit of gassiness. Ive tried several different brands of rolled oats. I might try briefly soaking next time and see if that helps. Overall this is a really filling transportable breakfast. And it is pretty low in sugar per muffin. Great recipe for those on kidney stone diets ( low oxylate low sodium and within added sugar goals) – bonus!.4 stars

  7. I’m gonna be honest, I’ve only tasted the batter because these are still in the oven, but nonetheless I am confident these are gonna be incredible. I replaced the egg with banana as we are egg free, and did half the honey as well as added a 1/4 cup applesauce to make up for the reduced honey. The batter is fantastic, I am so excited to eat these for breakfast!!!5 stars

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