Made with pumpkin puree, applesauce, and whole wheat, these healthier pumpkin muffins are perfect for quick breakfasts or an afternoon snack.
You might also like my pumpkin chocolate chip muffins, pumpkin pretzel bites, and pumpkin cinnamon swirl bread.

My kids get bored with sandwiches in their lunch, so I often find myself baking a batch of muffins in the evening to add to lunches the next day. This recipe is an adaptation of the one that I use for pumpkin mini loaves and pumpkin bread. It is so versatile!
Why I Like This Recipe
- Made with applesauce. Applesauce is a wonderful substitute for fat in muffin recipes. ½ cup applesauce = 110 calories; ½ cup vegetable oil = 960 calories. Applesauce adds moisture to the recipe while cutting out calories, fat, sodium, and cholesterol.
- Whole wheat flour. I don't care for the flavor of whole wheat flour on its own, so I always use a 50/50 blend with all-purpose flour, but you can definitely make these with 100% whole wheat flour.
- Versatile muffin recipe. Add nuts, carob chips, raisins, or dates! This is a versatile recipe that can be adjusted to your taste.
What Others Are Saying
Great recipe. I didn't know you substitute apple sauce for oil. Thanks!---Victoria
Just made these...substituted stevia for the sugar to reduce the Weight Watchers points. So good!!!! I've been craving all the pumpkin baked goods and these were perfect!---Dawn
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Tips and Tricks
- You don't need a stand or an electric mixer. You can make muffins and quick breads with a mixing bowl and Danish dough whisk or in a stand mixer. I have both and tend to mix by hand these days. I highly recommend using a Danish dough whisk over a wooden spoon. It works great to mix up batter and dough.
- Sugar substitutes. I experimented with maple syrup, but it didn't work out well in this recipe. If you want to keep the same flavor and consistency as a traditional pumpkin muffin, I do not recommend making any sugar substitutes. I don't have experience baking with Stevia, but I have had readers report great results using it in place of sugar.
Ingredients

- All-purpose flour and whole wheat flour: I don't care for the flavor of whole wheat flour on its own, so I always use a 50/50 blend with all-purpose flour, but you can definitely make these with 100% whole wheat flour.
- Baking powder, baking soda, and salt: For leavening and texture.
- Cinnamon and pumpkin spice: Pumpkin pie spice contains cinnamon already, but I like adding a bit more. You can also create your own spice mix of cinnamon, nutmeg, cloves, and ginger.
- Sugar: I tried making these with maple syrup and was very disappointed in the flavor and texture. Sugar is so much better, so that is one ingredient that I wasn't willing to sacrifice. Stevia or monk fruit could also be used.
- Pumpkin puree: 100% canned or fresh pumpkin puree, not pumpkin pie filling.
- Applesauce: Applesauce adds moisture to the recipe while cutting out calories, fat, sodium, and cholesterol.
- Eggs
- Vanilla
- Add-ins: Try adding walnuts, pecans, or dates.
See the recipe card for full information on ingredients and quantities.
How To Make Healthier Pumpkin Muffins

Step 1: Whisk flour, spices, baking soda, baking powder, and salt together in a mixing bowl.

Step 2: Combine sugar, pumpkin, eggs, applesauce and vanilla in a seperate bowl.

Step 3: Mix wet and dry ingredients together. Feel free to add mix-ins like nuts or carob chips.

Step 4: Scoop batter into a greased muffin pan or muffin pan with muffin liners.

Step 5: Bake muffins at 350 degrees for 20 minutes. Allow muffins to cool in the pan for 5-10 minutes before transferring to a cooling rack.
Pumpkin Muffins FAQs
I experimented with maple syrup, but it didn't work out well in this recipe. If you want to keep the same flavor and consistency as a traditional pumpkin muffin, I do not recommend making any sugar substitutes. I don't have experience baking with Stevia, but I have had readers report great results using it in place of sugar.
Store in an air tight container at room temperature up to 3 days. They can also be stored in the freezer for a month or two.
Yes, you can use whole wheat flour in this pumpkin muffin recipe. I prefer a 50/50 blend of all-purpose flour and wheat flour for the best flavor and texture.

More Muffin Recipes
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Healthier Pumpkin Muffins
Ingredients
- ¾ cup all purpose flour
- ¾ cup whole wheat flour
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- 1 ½ teaspoons ground cinnamon
- 1 ½ teaspoons pumpkin pie spice
- 1 cup sugar or sugar substitute
- 1 cup pumpkin puree
- ⅓ cup applesauce
- 2 eggs
- 1 teaspoon vanilla
- 1 cup chopped walnuts optional
Instructions
- In a large bowl, mix flour, spices, baking soda, baking powder, and salt.
- Mix eggs, applesauce, pumpkin, and vanilla together in a separate bowl.
- Mix dry and wet ingredients together. Add nuts, if desired.
- Line a muffin pan with 12 baking liners. Divide batter into 12 muffin liners.
- Bake at 350 degrees for 20 minutes (or until a toothpick inserted comes out clean). Let muffins cool in the muffin pan for a few minutes before transferring to a wire rack to cool.









Amy says
I love cinnamon and pumpkin and these muffins sound delicious. Thank you for sharing at Wonderful Wednesday.
victoria james says
Great recipe. I didn't know you substitute apple sauce for oil. Thanks!
Dawn Beaver says
Just made these...substituted stevia for the sugar to reduce the Weight Watchers points. So good!!!! I've been craving all the pumpkin baked goods and these were perfect!
Brandy says
This is so good to know! I JUST had a reader ask if she could substitute the sugar for sweetener for another pumpkin recipe that I have, but I hadn't ever tried and wasn't sure what to tell her!
Dawn says
Yes! They were delicious!!
JESS44903 says
Pinned! These sound amazing!
I would love for you to share this with my Facebook Group for recipes, crafts, tips, and tricks: https://www.facebook.com/groups/pluckyrecipescraftstips/
Thanks for joining Cooking and Crafting with J & J!
Kim says
I so didn't know you could trade applesauce for oil! I'll have to try it! Thank you for sharing on Merry Monday! Hope to see ya next week!
Kim
Florence says
Why is it that I'm always looking at recipes, when I'm starving...LOL! These muffins look so good, and I know they are good b/c I see those ingredients, and they are my faves too. Love that it's made with applesauce, which tastes just as good as oil, IMO. Thanks for sharing at Sweet Inspiration!
Simone Emery says
These look great and perfect for lunchboxes 🙂
Carrie says
Those looks delish! Pinning.
Miz Helen says
We will just love your Cinnamon Pumpkin Muffins, they look awesome. Hope you have a great week and thanks so much for sharing with Full Plate Thursday.
Miz Helen
Christine @ www.rustic-refined.com says
That looks wonderful Brandy! Thanks so much for joining us at the DI & DI Link party.
JESS44903 says
This sounds so tasty! PINNED! 🙂
I would love for you to share this with my Facebook Group for recipes, crafts, tips, and tricks: https://www.facebook.com/groups/pluckyrecipescraftstips/
Thanks for joining Cooking and Crafting with J & J!
Easy Peasy Life Matters says
This sounds so perfect for breakfast or dessert!!! 🙂
Emily says
My mouth is watering right now! These sound like a perfect bite of fall flavors! Thanks for linking up with Merry Monday this week.
Emily says
I'm visiting from Your Whim's Wednesday. These look great! I bet my kids would love them, too; and I'm all for my house smelling fallish!! Thanks for sharing!
thefirsttastekc says
Great recipe! I can't wait to try it, thanks for sharing!