Healthy Pumpkin Muffins - Eating Bird Food

These healthy pumpkin muffins are moist, fluffy and delicious! They’re naturally sweetened and made with whole wheat flour, rolled oats, yogurt and fall spices.

The weather is finally starting to feel like fall and I couldn’t be more excited! I love all things fall… apple picking, pumpkin spice lattes and my favorite of all… fall baking! There’s just something about the cozy spices and warm treats that I can’t get enough of. Some of my go-to recipes are these baked apple cider donuts, healthy apple muffins and of course, these delicious healthy pumpkin muffins.

I have shared a few pumpkin muffin recipes over the years like my vegan pumpkin muffins and flourless pumpkin muffins, but I wanted to share more of a classic pumpkin muffin recipe that’s a bit healthier.

Multiple pumpkin muffins near one another with some stacked on top of others.

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Why You’ll Love These Muffins

Healthier – These muffins are naturally sweetened, made with whole wheat flour and rolled oats and use Greek yogurt to replace some of the oil. No refined sugars or flour over here!
Easy to Make – This recipe is super easy to make and I bet you already have all the ingredients on hand. From start to finish these muffins take about 30 minutes to whip up.
Perfect Texture – These muffins come out soft, moist and oh-so fluffy!
Festive – It’s the perfect fall recipe You’ll love the slightly sweet pumpkin flavor of these muffins thanks to the pumpkin puree and pumpkin spice.

Ingredients Needed

Ingredients measured out to make Healthy Pumpkin Muffins: whole wheat pastry flour, eggs, sea salt, baking soda, pumpkin pie spice, oats, vanilla, honey, Greek yogurt, pumpkin and avocado oil.

whole wheat pastry flour or white whole wheat flour – whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy bread that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour. If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
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 – make your own pumpkin pie spice at home or use a store-bought blend.
baking soda – to help the muffins rise.
pumpkin puree – you can use canned pumpkin or homemade pumpkin puree. If using store-bought, just make sure the ingredient list is only “pumpkin” – you don’t want to accidentally buy pumpkin pie filling, which has added sugars.
eggs – helps bind the wet and dry ingredients together and gives these muffins 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

A large bowl of pumpkin puree, eggs, honey, and vanilla.

Step 1: Preheat your oven and whisk together the pumpkin puree, honey, greek yogurt, oil, eggs and vanilla in a large bowl.

A large bowl of all the dry ingredients used for pumpkin muffins.

Step 2: Add the flour, oats, pumpkin pie spice, baking soda and salt in a medium mixing bowl. Stir to fully combine.

A woman's hand uses a silicone spatula to fold the wet and dry ingredients for pumpkin muffins together.

Step 3: Add the dry ingredients into the bowl with the wet ingredients and mix until just combined.

Twelve pumpkin muffins in a muffin tin after being baked.

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.

Brittany’s Tips!

Don’t over-mix: When mixing the batter, don’t stress about getting it perfectly smooth. It’s totally fine if you see a few clumps—that’s actually a good thing! Over-mixing can make your muffins tough, so once everything is mostly combined, just stop stirring. Those little clumps will bake out, and you’ll be left with soft, fluffy muffins.
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.

A pumpkin muffin with a bite taken from it near other muffins.

What to Serve with Healthy Pumpkin Muffins

These pumpkin muffins are the perfect simple breakfast or afternoon snack. Here are some serving ideas:

Six pumpkin muffins in a muffin tin. The muffins are topped with rolled oats.

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

How do I prevent the muffins from sticking to the liners?

Make sure you grease the muffin liners with nonstick spray before adding the batter, or use silicone muffin liners which are naturally nonstick.

Why are my pumpkin muffins dry?

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.

Can I add a mix-in to these muffins?

Yes! 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.

Can I freeze these muffins?

Definitely! These muffins store really well in the freezer. Just let them cool completely then transfer them to an airtight freezer-safe container or bag for storage. They can be stored in the freezer for up to 3 months. To thaw, place them in the fridge overnight.

More Pumpkin Recipes to Try

Be sure to check out the full collection of pumpkin recipes and all my muffin recipes here on EBF.

If you enjoyed this recipe, please consider leaving a ⭐ star rating and let me know how it went in the 📝 comments below.

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.

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!
Optional mix-ins: You could add some chopped nuts, chocolate chips or dried cranberries to the batter. 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.

Nutrition information is automatically calculated, so should only be used as an approximation.

Healthy Pumpkin Muffins – Eating Bird Food