Healthy Pumpkin Muffins
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These 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.
The weather is finally starting to feel like fall and I couldn’t be more excited! Once pumpkin season hits, I’m all in with cozy sweaters, apple picking, baking these healthy pumpkin muffins, and sipping on my favorite pumpkin spice latte. There’s just something about the smell of warm pumpkin spice filling the kitchen that makes everything feel extra cozy. These muffins are soft, fluffy, and full of that classic fall flavor I love.
Table of Contents
Why I Love These Pumpkin Muffins
- Healthier – These muffins are naturally sweetened and made with whole wheat flour, rolled oats, and Greek yogurt in place of most of the oil. No refined sugar or white flour here.
- Easy to make – The batter comes together fast with ingredients you probably already have in your pantry. From start to finish, they’re ready in about 30 minutes.
- Perfect texture – Soft, fluffy, and just the right amount of moisture in every bite.
- Festive – Full of pumpkin puree and warm spices, these muffins bring that cozy fall flavor that makes your kitchen smell amazing.
“Love these! I make them at least 10+ times a year. They freeze well, always come out moist and soft…”
Ingredients Needed
- whole wheat pastry flour or white whole wheat flour – whole wheat pastry flour gives these muffins that light, fluffy texture while still adding nutrients. I like Bob’s Red Mill whole wheat pastry flour best. If you can’t find it, white whole wheat flour or even regular all-purpose flour will work.
- old fashioned rolled oats – my fave brand is Bob’s Red Mill gluten-free old fashioned rolled oats. We’ll mix some into the batter and top the muffins with some extra oats.
- pumpkin pie spice – brings all the warm fall flavors together. You can use a store-bought blend or make your own with cinnamon, nutmeg, ginger and cloves.
- baking soda – to help the muffins rise.
- pumpkin puree – the star of the show! Use pure pumpkin puree (not pumpkin pie filling) for the best flavor and texture.
- eggs – binds the batter together and adds structure.
- honey or maple syrup – we tested this with ½ cup of maple syrup and then with ¾ cup honey. We liked the honey version much better, but if you want the muffins less sweet, feel free to reduce the sweetener to ½ cup.
- Greek yogurt – plain non-fat Greek yogurt keeps these muffins moist without a lot of added oil.
- avocado or olive oil – you only need 2 Tablespoons of oil for the whole batter.
Find the full ingredient list with measurements in the recipe card below.
Recipe Substitutions
- Add mix-in’s: I love these muffins as is but if you want to add some texture you could mix in some walnuts or pecans. Want a little extra sweetness? Add in chocolate chips or dried cranberries.
- Make them gluten-free: I haven’t tested these with a gluten-free flour mix but you should be able to swap a gluten-free all purpose blend for the flour in this recipe. Or try this tested and approved flourless pumpkin muffin recipe.
- Need a vegan recipe? Try my vegan pumpkin muffins instead!
How to Make Healthy Pumpkin Muffins
Follow these simple steps to make the best healthy pumpkin muffins. Everything comes together fast, and before you know it your kitchen will smell like fall.
Step 1: Preheat your oven and whisk together the pumpkin puree, honey, greek yogurt, oil, eggs and vanilla in a large bowl.
Step 2: Add the flour, oats, pumpkin pie spice, baking soda and salt in a medium mixing bowl. Stir to fully combine.
Step 3: Add the dry ingredients into the bowl with the wet ingredients and mix until just combined.
Step 4: Divide the batter evenly between the 12 muffin cups. Sprinkle a few oats on the tops of each muffin. Bake for 22-24 minutes, or until a toothpick inserted comes out clean.
Tips for the Best Pumpkin Muffins
- Don’t over-mix: Stop stirring once everything is mostly combined. A few lumps are totally fine! Over-mixing can make your muffins dense instead of soft and fluffy.
- Use silicone or paper liners: These make for easy removal and less mess. If you don’t have liners, make sure to thoroughly grease the muffin tins. These are my favorite silicone muffin cups.
How to Store
These muffins store really well. Store them in an airtight container at room temperature for 2-3 days or in the refrigerator for 4-5 days. You can also freeze these for longer storage. I recommend using a freezer-safe container and storing them for up to 3 months.
Frequently Asked Questions
Make sure you grease the muffin liners with nonstick spray before adding the batter, or use silicone muffin liners which are naturally nonstick.
Over-baking is a common reason for dry muffins. Make sure to check them a few minutes before the suggested baking time and remove them from the oven as soon as a toothpick comes out clean.
I kept these muffins plain, but you can absolutely add mix-in’s to the batter. Some ideas are chocolate chips, dried fruit and/or nuts. I would keep the total amount of mix-ins around 1/2 cup. Add them to the batter last, after you’ve combined the wet and dry ingredients.
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.
Healthy 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 pure vanilla extract
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.
- Combine the flour, oats, pumpkin pie spice, baking soda and salt in a medium mixing bowl.
- 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.
- Place the muffin tin on a cooling rack to cool. Once cool enough to handle, remove from the muffin tin and to cool completely.
- They’ll keep at room temperature for up to 2-3 days, or in the refrigerator for 4-5 days. They keep well in the freezer in a freezer-safe container for up to 3 months.
Notes
- Want to make these lower in sugar? We tested this with ½ cup of maple syrup and then with ¾ cup honey. We liked the honey version much better, but if you want the muffins less sweet, feel free to reduce the sweetener to ½ cup.
- Need this recipe to be gluten-free? You should be able to swap a gluten-free all purpose blend for the whole wheat pastry flour or try this tested and approved flourless pumpkin muffin recipe!
- Need a vegan recipe? Try my vegan pumpkin muffins instead!
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!
Amazing! Easy and delicious. Freezes well. Totally festive and delightful!
Amazing! This makes me so happy to hear, Renee. Thank you for giving this recipe a try and for sharing your review + star rating, it means so much to me!
I tried these muffins but I used half ww pastry flour and half oatmeal flour because I did’nt have enough pastry flour. they were so nice and moist and absolutely delicious. they did’nt last long.
WOO! Glad you loved this muffins and they turned out amazing for you, Terrie. Thanks so much for sharing your review + star rating, I truly appreciate it!
This was my second time making this. Delicious! My teenage son ate 3 pieces yesterday. I added oatmilk chocolate chips and made my own pumpkin puree. I know I will be making it again.
So yummy! I made with oat flour and brown sugar. I also added walnuts. They turned out great! Thanks for the great recipe.
Perfect! I am so happy to hear that these turned out great for you with your subs, Liz. Thanks so much for coming back and sharing your review + star rating, I truly appreciate it!
1)the oats did not cook and were tough
2)while the outside rose and browned nicely the inside was gummy and soggy
4)how about a version using allulose, stevia or erythritol instead of high calorie sweetener
Hi Margie – Did you change anything about the recipe? What type of oats did you use? You can definitely adjust the sweetener using whatever you prefer.
Looking to make these… has anyone tried using regular yogurt or non-dairy yogurt (my fav is Cashewgurt) instead of the Greek Yogurt?? Wondering if it would change recipe much at all… lmk please if you’ve tried this! 🙂
I think these muffins would be just fine with dairy-free yogurt! Let me know if you try it and how they turn out.
I wonder if this can be made into a loaf instead how long do you think it would be in oven for?
Hey Mary – I think it would turn out as a loaf instead of muffins! I’d guess it would take 40-50 minutes, but I’d keep an eye on it. 🙂 Let me know how it turns out if you try it!
Question! Can I replace the flour for Einkorn all purpose flour?
I’ve never tried Einkorn flour, but I’d imagine it would work just fine! Let me know if you try it!
I’m going to try this today but try subbing some of the flour, about 1/2c with protein powder. What are your thoughts?
I haven’t tried it so not sure if it’ll change the consistency of the muffins. Keep me posted how they turn out!
They turned out very good. I used spelt flour,1banana in place of the maple syrup, coconut oil also added walnuts. Very filling breakfast, not sure what I’ve done to the nutrition breakdown.
Happy to hear you enjoyed these pumpkin muffins, Valerie! Thanks for the review 🙂
I was so excited to see this recipe, as I’m always looking for low sugar, clean, healthy recipes for my husband and I. I tried this recipe today and was not happy with the result. The only items I changed were cutting back to 1/4 cup of sweetener and I used Bob’s Red Mills Gluten Free Flour. The consistency was not as pictured and was thinking that more wet ingredients were needed. Would greatly appreciate your thoughts. Thanks l!
Oh no!! So sorry to hear that, Eileen. What sweetener did you use? I’m wondering if it needed a bit more liquid since you cut back the sugar to 1/4 cup vs. 1/2-3/4 cup.