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.









Brandy says
Hi everyone! Brandy here, these muffins and moist and delicious and a bit healthier since they are made with applesauce vs. butter/oil. They make a yummy, quick breakfast.
Joyce says
Can I use in mini loaf pans?
Brandy says
Hi Joyce! You can definitely use mini loaf pans. You'd just need to adjust the baking time to probably 25 minutes or so.
Cortne Trout says
Pinned for later! Thanks for sharing!!