Healthy Pumpkin Muffins
Posted Oct 04, 2020, Updated Oct 21, 2022
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These are the best healthy pumpkin muffins ever! They’re tender and moist with a beautiful crumb, naturally sweetened, perfectly spiced and made with whole wheat flour but you’d never guess they’re good for you! This healthy pumpkin muffin recipe is easy to make in 30 minutes, and is a nutritious fall breakfast!
Fall baking is my favorite (hello pumpkin bread), but sometimes I want to make lighter versions of my favorite recipes, like these Healthy Pumpkin Muffins. They’re tender and moist with a beautiful crumb, naturally sweetened, perfectly spiced and made with whole wheat flour but you’d never guess they’re good for you!
This healthy pumpkin muffin recipe is easy to make in 30 minutes – including baking time. You can top them with raw sugar (or not), or add your favorite mix-ins to make them extra-special! Serve them warm with a generous slather of this homemade cinnamon honey butter and you’ll experience breakfast nirvana!
Healthy Pumpkin Muffin Recipe: Ingredients & Substituions
- Pumpkin Puree. Be sure to use pure pumpkin puree (not pumpkin pie filling). Fresh or canned both work well.
- Salted Butter. Unsalted butter, coconut oil, ghee, etc. can be used in place of salted butter if desired.
- Vanilla Greek Yogurt. Any yogurt variety works well in this healthy pumpkin muffin recipe. I prefer vanilla Greek yogurt for the extra protein, flavor and sweetness. I also love using vanilla bean Icelandic yogurt!
- Maple Syrup. I’ve used honey in place of maple syrup with great results, however I prefer syrup because the maple flavor screams “fall.”
- Eggs. You can use chia or “flax” eggs by combining 2 TBS ground chia seeds or flaxseed meal and 5 TBS warm water and letting it set for 10 minutes, then use in the recipe. The muffins might bake flatter if you do this.
- Whole wheat flour. All-purpose, spelt, whole wheat pastry flour, white whole wheat flour, etc. can be used in place of regular whole wheat flour.
- Pumpkin Pie Spice. Use store bought or make your own with this recipe: homemade pumpkin pie spice.
- Raw sugar. This is optional, but I love the extra shine and crunch a sprinkle of raw sugar gives to the tops of these healthy pumpkin muffins.
- Mix-ins. You can add up to 1 cup of mix-ins of your choice, I will discuss options later in this post!
How to make Healthy Pumpkin Muffins
This healthy pumpkin muffin recipe is easy to make and takes 30 minutes from start to finish. As always, we’ll walk through the recipe step-by-step, and don’t forget to watch the video.
Combine dry ingredients.
In a medium bowl, combine whole wheat flour, cinnamon, pumpkin pie spice, baking powder, baking soda and sea salt. Set aside.
Homemade Pumpkin Pie Spice
If you’d like to make your own pumpkin pie spice, use this recipe: homemade pumpkin pie spice. Then use 2 tsp of the mixture in the recipe and save the rest for your other pumpkin recipe endeavors (like this pumpkin pie, paleo pumpkin bread, or pumpkin baked oatmeal).
Whisk together wet ingredients
In a large bowl, whisk together pumpkin puree, melted butter, yogurt, maple syrup, eggs and vanilla until smooth.
Add dry ingredients
Once the wet ingredients are smooth, add the dry ingredients and stir until mixture is smooth and there are no lumps.
Optional: Add mix ins
If desired, add mix-ins of your choice, here are some suggestions:
- Chocolate chips
- Cinnamon chips (YUM)
- White chocolate chips
- Dried cranberries or rasins
- Nuts: pecans, walnuts, etc.
Portion into muffin tin
Measure 3-4 TBS of batter into each well of a standard muffin in. If desired, sprinkle the tops of the muffins with raw sugar.
I prefer to generously grease my muffin tins instead of using cupcake liners, but you may bake them either way.
Bake
Bake the healthy pumpkin muffins in the preheated oven for 17-20 minutes, or until the tops spring back when touched and a toothpick inserted in the center of the muffins comes out clean or with a few moist crumbs.
Cool
Let cool in the pan for 2-5 minutes. Then transfer to a wire rack to cool completely, using a spoon or knife to release the sides from the pan and gently remove them.
Serve!
Serve these healthy pumpkin muffins warm with a generous slather of cinnamon honey butter, homemade peanut butter, or homemade vanilla almond butter.
Store
Store these healthy pumpkin muffins in an airtight container at room temperature for up to 3 days, or in the refrigerator for up to 1 week.
How to freeze healthy pumpkin muffins:
- Let muffins cool completely
- Transfer to an airtight container or freezer-friendly plastic bag.
- Transfer to the freezer and freeze for up to 2 months.
To reheat:
Reheat the healthy pumpkin muffins in one of three ways:
- Warm in the microwave for about 40 seconds per muffin.
- Remove from the freezer and let them thaw to room temperature overnight.
- Warm in the oven preheated to 325 degrees F for about 5-10 minutes or until warmed through.
Recipe FAQs
These muffins last for up to 3 days at room temperature, 1 week in the refrigerator, and 2 months in the freezer. Make sure they’re always in an airtight container to prevent drying out.
I like to serve these with a slather of homemade cinnamon butter, and on the side of a savory dish like this egg casserole. Always with a warm cup of coffee!
They don’t need to be refrigerated but I recommend it because they last longer that way. Reheat for a few seconds in the microwave to restore their from-the-oven warmth and texture.
Yes, they are fine when left overnight in an airtight container.
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Healthy Pumpkin Muffins
Ingredients
- 1 cup pumpkin puree
- ¼ cup salted butter melted
- ½ cup vanilla Greek yogurt
- ½ cup maple syrup or honey
- 2 eggs
- 1 tsp pure vanilla extract
- 1 ½ cups whole wheat flour
- 2 tsp ground cinnamon
- 2 tsp pumpkin pie spice
- 1 tsp baking powder
- ½ tsp baking soda
- ½ tsp sea salt
- 4 TBS raw sugar for sprinkling optional
- Optional: 1 cup of mix ins.
Instructions
- Preheat oven to 375 degrees F. Lightly grease a standard, 12-cup muffin tin. Set aside.
- In a medium bowl, combine whole wheat flour, cinnamon, pumpkin pie spice, baking powder, baking soda and sea salt. Set aside.
- In a large bowl, whisk together pumpkin puree, melted butter, yogurt, maple syrup, eggs and vanilla until smooth.
- Add dry ingredients and stir until mixture is smooth and there are no lumps.
- If desired, add mix-ins (chocolate chips, nuts, seeds, etc.).
- Measure 3-4 TBS of batter into each cup of the prepared muffin tin. If desired, sprinkle the tops of the muffins with raw sugar.
- Bake in the preheated oven for 17-20 minutes, or until the tops spring back when touched and a toothpick inserted in the center of the muffins comes out clean.
- Let cool in the pan for 2-5 minutes. Then transfer to a wire rack to cool completely.
- Serve!
Video
Notes
Ingredient Substitutions
- Pumpkin Puree. Fresh or canned both work well.Â
- Salted Butter. Unsalted butter, coconut oil, ghee, etc. can be used in place of salted butter if desired.Â
- Vanilla Greek Yogurt. Any yogurt variety works well. My top preferences are Greek and Icelandic yogurts for their thickness and creaminess.Â
- Maple Syrup. I’ve used honey in place of maple syrup with great results.
- Eggs. You can use chia or “flax” eggs by combining 2 TBS ground chia seeds or flaxseed meal and 5 TBS warm water and letting it set for 10 minutes, then use in the recipe. The muffins might bake flatter if you do this.Â
- Whole wheat flour. All-purpose, spelt, whole wheat pastry flour, white whole wheat flour, etc. can be used in place of regular whole wheat flour.
- Pumpkin Pie Spice. Use store bought or make your own with this recipe:Â
- 1 ½ tsp cinnamon
- ½ tsp nutmeg
- ½ tsp cloves
- ½ tsp allspice
Store
Store these healthy pumpkin muffins in an airtight container at room temperature for up to 3 days, or in the refrigerator for up to 1 week.ÂHow to freeze healthy pumpkin muffins:Â
- Let muffins cool completely
- Transfer to an airtight container or freezer-friendly plastic bag.
- Transfer to the freezer and freeze for up to 2 months.Â
To reheat:Â
Reheat the healthy pumpkin muffins in one of three ways:- Warm in the microwave for about 40 seconds per muffin.Â
- Remove from the freezer and let them thaw to room temperature overnight.
- Warm in the oven preheated to 325 degrees F for about 5-10Â minutes or until warmed through.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
If you love this recipe, try these:
- Paleo pumpkin muffins or paleo pumpkin bread are delicious, gluten-free fall baking recipes.
- Pumpkin baked oatmeal and pumpkin overnight oats are more delicious and healthy fall breakfast recipes!
- This is the best pumpkin bread recipe ever!
- PIE! If you haven’t dried our from-scratch pumpkin pie or dairy free pumpkin pie they are must-makes this fall.
- This no bake vegan pumpkin cheesecake is healthy and delicious!
- For a treat, try these pumpkin cinnamon rolls or these pumpkin pancakes.
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Made these yummies for the first time, and they were very good. Put in some flaxseed meal and used some pumpkin yogurt, and they were awesome.
Thank you, Melissa!
Absolutely awesome! Didn’t change a thing. 3 tb per muffin.
Made these today. Love them! Full of flavor and super moist! And they are healthier! All the recipes look so good, I know I will be coming back here when I am looking for one.
Thank you Laura! Happy to have you here! Hope to cook with you for years to come! 🙂
Hello I would love to make this as a loaf cake how long would I bake it for and what temperature?
These are very good and I made them as stated. I used salted butter, real eggs, King Arthur Measure for Measure gluten free flour, canned pumpkin and made the pumpkin pie spice mix. I added raisins and chopped walnuts also.
The spice ratio is outstanding. It made 12 muffins.
Also maple syrup, and plain greek yogurt. Not vanilla but I added vanilla extract.
Wow amazing! I made it dairy free with an overripe banana and added a little unsweetened applesauce. I used a cashewmilk vanilla yogurt made by forager instead of greek yogurt. It’s not too pumpkin flavored it was great! I made tiny muffins to try out my new muffin tin and they were done in about 16-17 minutes. Thank you!
Tried this recipe………Very tasty muffins……Kids loved them ……….Even with whole wheat flour, they were quite good