Healthy Pumpkin Muffins
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Add as Google Trusted SourceThese healthy pumpkin muffins are soft, fluffy and full of cozy fall flavor. Made with Greek yogurt, oats and whole wheat pastry flour, they’re lightly sweet and perfect for breakfast or an afternoon treat.
These healthy pumpkin muffins are my kind of fall baking: simple ingredients, plenty of pumpkin spice and no mixer to pull out of the cabinet. I love using Greek yogurt in the batter because it keeps the muffins moist and tender with just a little oil. Add whole wheat pastry flour and rolled oats, and you’ve got a muffin that’s hearty enough for breakfast but still soft and fluffy.
If you’ve tried my healthy pumpkin bread, these belong right alongside it in your fall baking rotation. And don’t skip the sprinkle of oats on top! It’s a simple finishing touch, but I love how it makes each muffin look a little more special.
Table of Contents
“Love these! I make them at least 10+ times a year. They freeze well, always come out moist and soft…”
Why I Love These Pumpkin Muffins
- No mixer needed: A couple of bowls, a whisk and a spoon are all you need to pull the batter together.
- Save some for later: The recipe makes 12 muffins, so you can freeze a few for mornings when baking isn’t happening.
- A coffee-shop treat at home: Pair one with my homemade pumpkin spice latte for a little fall breakfast moment without the coffee-shop stop.
Ingredients Needed
- whole wheat pastry flour – keeps the crumb lighter than regular whole wheat flour. Bob’s Red Mill is my go-to.
- rolled oats – adds a little chew to the muffins. I use Bob’s Red Mill old-fashioned rolled oats.
- pumpkin pie spice – brings the cinnamon, ginger and other warm spices together in one convenient blend.
- baking soda – helps the muffins rise. Check that yours is fresh, especially if it’s been sitting in the pantry since last fall!
- pumpkin puree – the star of the show! Use pure pumpkin puree (not pumpkin pie filling) for the best flavor and texture.
- honey or maple syrup – naturally sweetens the muffins. We tested a batch with ½ cup maple syrup and another with ¾ cup honey, and preferred the honey batch! For a less sweet muffin, use ½ cup sweetener.
- Greek yogurt – plain nonfat Greek yogurt is what I use here. Choose an unsweetened variety so you aren’t adding extra sweetness or flavor.
- eggs – binds the batter together and adds structure.
- avocado or olive oil – avocado oil has a neutral flavor. If using olive oil, choose a mild-tasting one.
Find the full ingredient list with measurements in the recipe card below.
Recipe Substitutions
- Add chocolate or fruit: Fold in up to ½ cup chocolate chips or dried cranberries for little pockets of sweetness.
- Add nuts: Walnuts or pecans are a good option if you want some crunch. Keep the total mix-ins to about ½ cup if combining nuts with chocolate or dried fruit.
- Need gluten-free muffins? I haven’t tested a gluten-free flour blend in this recipe. My flourless pumpkin muffins are a tested option made without wheat flour.
- Need an egg-free, dairy-free option? My vegan pumpkin muffins are already developed that way, so you won’t need to juggle several substitutions.
How to Make Healthy Pumpkin Muffins
Step 1: Preheat the oven to 350°F and prepare a 12-cup muffin pan. Whisk the pumpkin, sweetener, yogurt, oil, eggs and vanilla together in a large bowl.
Step 2: In a separate bowl, stir together the flour, oats, pumpkin pie spice, baking soda and salt.
Step 3: Gently fold the dry ingredients into the wet mixture just until no dry flour remains.
Step 4: Divide the batter evenly among the muffin cups and sprinkle with extra oats. Bake for 22–24 minutes, until a toothpick inserted into the center comes out clean. Let cool slightly before transferring to a wire rack.
Tips for the Best Pumpkin Muffins
- Spoon and level your flour: Scooping directly from the bag can pack too much flour into the measuring cup. Spoon it in loosely, then level the top with a knife to avoid a dry, heavy muffin.
- Don’t chase a perfectly smooth batter: The oats will leave some texture, and that’s okay! Trying to stir out every lump can overwork the batter and make the muffins tough.
- Give your liners a little help: Lightly spray paper liners with nonstick spray for easier release, or use silicone muffin cups. Let the muffins cool before peeling away the liners.
How to Store Pumpkin Muffins
Storage: Once completely cool, keep the muffins in an airtight container at room temperature for 2–3 days or in the refrigerator for 4–5 days. A paper towel in the container helps absorb excess moisture. Replace it if it becomes damp.
Freezing: Wrap the cooled muffins individually and place them in a freezer-safe bag or container for up to 3 months.
Thawing: Unwrap a muffin and let it thaw at room temperature, or microwave in short intervals until warmed through.
Frequently Asked Questions
Yes! All-purpose flour or white whole wheat flour can replace the whole wheat pastry flour. White whole wheat is still a whole-grain flour, despite its lighter color and milder flavor.
I haven’t tested regular yogurt in this recipe. It’s thinner than Greek yogurt and could change the batter’s consistency, so I recommend sticking with Greek yogurt for the most predictable results.
They may need more baking time, especially if the outside looks done before the center has set. Check a muffin near the middle of the pan with a toothpick before taking the batch out. Measure the pumpkin carefully, since extra puree adds moisture, and let the muffins cool before judging their final texture.
More Pumpkin Recipes You’ll Love
If you enjoyed this recipe, please consider leaving a ⭐ star rating and let me know how it went in the 📝 comments below.
Greek Yogurt Pumpkin Muffins
Ingredients
- 1 ½ cup whole wheat pastry flour , or white whole wheat flour
- ½ cup old fashioned rolled oats, plus more for topping muffins
- 2 teaspoons pumpkin pie spice
- 1 teaspoon baking soda
- ½ teaspoon sea salt
- 1 cup canned pumpkin or homemade pumpkin puree
- ¾ cup honey or maple syrup
- ½ cup Greek yogurt
- 2 Tablespoons avocado or olive oil
- 2 eggs
- 1 teaspoon vanilla
Instructions
- Preheat oven to 350°F. Line a muffin tin with silicone or paper liners.
- Whisk together the pumpkin puree, honey, Greek yogurt, oil, eggs and vanilla in a large bowl.1 cup canned pumpkin or homemade pumpkin puree, ¾ cup honey or maple syrup, ½ cup Greek yogurt, 2 Tablespoons avocado or olive oil, 2 eggs, 1 teaspoon vanilla
- Combine the flour, oats, pumpkin pie spice, baking soda and salt in a medium mixing bowl.1 ½ cup whole wheat pastry flour , ½ cup old fashioned rolled oats, 2 teaspoons pumpkin pie spice, 1 teaspoon baking soda, ½ teaspoon sea salt
- Add the dry ingredients into the bowl with the wet ingredients and mix until just combined. There may be a few lumps, that’s totally fine. Just don’t over mix!
- Divide the batter evenly between muffin cups. Sprinkle a few oats on the tops of each muffin.
- Bake muffins for 22 to 24 minutes, or until a toothpick inserted into a muffin comes out clean.
- Let the muffins cool slightly, then remove from the pan and transfer to a wire rack to cool completely.
Notes
- Sweetener: We tested these with ½ cup maple syrup and with ¾ cup honey, and preferred the honey batch. For less sweet muffins, reduce the sweetener to ½ cup.
- Flour: White whole wheat flour or all-purpose flour can replace the whole wheat pastry flour.
- Optional mix-ins: Fold in up to ½ cup total chocolate chips, dried cranberries, walnuts or pecans.
- Storage: Cool completely before storing in an airtight container. Keep at room temperature for 2–3 days, refrigerate for 4–5 days or freeze for up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Like This Recipe? Rate & Comment Below!
My kids loved these! I added a tablespoon of ground flaxseed and 1/2 c mini chocolate chips. Only used 1/2 c honey. Delicious and much healthier than what I used to make 🙂
Yay! So glad these muffins were a hit. Thanks for making them and for coming back to leave a review. I so appreciate it!
Love these! I make them at least 10+ times a year. They freeze well, always come out moist and soft and I’ve found with some trial and error some protein powders can be added without changing the consistency. I’ve tried mult Greek yogurt brands and all have worked well.
Yay! So glad you loved this recipe, Kristin. Thanks so much for making it and for coming back to leave a review. I really appreciate it.
These need a little more structure. They are very moist, but for my taste, a little too moist; I prefer a breadier texture. Unfortunately, not my favorite pumpkin muffin recipe.
Hi Fran – So sorry these didn’t hit the spot for you. Thank you for your feedback, I appreciate it!