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These healthy pumpkin spice muffins are one of my favorite ways to enjoy all those cozy fall flavors! They’re made with pumpkin puree and pumpkin pie spice, which gives them the perfect amount of pumpkin flavor and makes them so moist and tender. There’s no oil or butter, and everything comes together in one bowl, so they’re incredibly easy to make. I love making a batch for meal prep, and honestly, they’re so good, I have a feeling you’ll want to make them all season long!

For more easy and healthy pumpkin muffins, try my pumpkin chocolate chip muffins, pumpkin cream cheese muffins, and pumpkin oat muffins next!
Table of Contents
- 🔎 Quick Look: Healthy Pumpkin Spice Muffins
- Why You Will Love This Recipe
- Key Ingredients
- Substitutions & Variations
- How to Make Healthy Pumpkin Spice Muffins
- Expert Tips
- Serving Suggestions
- Storage Instructions
- Healthy Pumpkin Spice Muffins FAQs
- More Healthy Muffin Recipes to Try!
- Healthy Pumpkin Spice Muffins Recipe
🔎 Quick Look: Healthy Pumpkin Spice Muffins
- ⏱️ Prep Time: 10 minutes
- ⏱️ Cook Time: 25 minutes
- 🕒 Total Time: 35 minutes
- 🍽 Calories: ~93 kcal per muffin
- 👥 Servings: 12 muffins
- 🥣 Key Ingredients: Flour, pumpkin puree, applesauce, pumpkin pie spice, sweetener
- 👩🍳 Cook Method: Baked
- ⭐ Difficulty: Easy
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Why You Will Love This Recipe
- Delicious Fall Flavors: These muffins have the delicious flavors of fall! They are packed with pumpkin flavor and autumn spices.
- Fall Treat: You can enjoy these muffins all season long!
- Easy to Make: They are easy to make and are perfect for fall baking.
- Healthy Muffins: These pumpkin muffins are made with simple, lighter ingredients. There is no butter or oil in this recipe!
- Great Texture: These muffins have a wonderful texture and flavor!
“These are delicious!!! Legit the texture, the sweetness and flavor is amazing! MUST TRY!!”
– cindy
Key Ingredients

- Flour: These muffins are made with all-purpose flour.
- Pumpkin Pie Spice: The pumpkin pie spice give these muffins a delicious pumpkin spice flavor!
- Sweetener: Use brown sugar or a 1:1 sugar-free sweetener.
- Eggs: Whisk two eggs for this muffin recipe.
- Applesauce: Unsweetened applesauce keeps these muffins moist and tender. There’s no butter or oil needed!
- Pumpkin Puree: Use pumpkin puree, not pumpkin pie filling. The pumpkin puree gives these muffins a pumpkin flavor and keeps them moist. For another recipe with pumpkin puree, try my healthy pumpkin baked oats next!
Find the full list of ingredients and measurements in the recipe card below.
Substitutions & Variations
- Add Chocolate Chips: If you want chocolate flavor in these pumpkin muffins, fold some regular or sugar-free mini chocolate chips into the batter before baking the muffins. Or, try my pumpkin chocolate chip muffins!
- What Sweetener to Use: You can sweeten these muffins with brown sugar or a 1:1 sugar replacement such as Swerve brown sugar or brown monk fruit.
- Mix-Ins: For another flavor and texture in these muffins, fold up to 1/2 cup of chopped walnuts or pecans into the batter. Or, you could fold in up to 1/2 cup of roughly chopped dried cranberries for a tart contrast to the sweet pumpkin.
- Oat Flour Option: You can even make these muffins with oat flour! Replace the all-purpose flour with 1 and 1/2 cups of oat flour. If needed, add a splash of milk as oat flour absorbs more liquid. Or, try my pumpkin oat muffins!
How to Make Healthy Pumpkin Spice Muffins

- Add the flour, baking soda, pumpkin pie spice, and brown sugar or Swerve brown sugar to a large bowl. After that, mix these ingredients.

- Add the whisked eggs, vanilla extract, unsweetened applesauce, and pumpkin puree to the bowl. After that, thoroughly combine the batter, but don’t over-mix.

- Pour the batter into a non-stick muffin pan, bake the muffins, and enjoy!
Expert Tips
- Use Pumpkin Puree: Use pumpkin puree for this recipe, not pumpkin pie filling. Pumpkin pie filling contains added spices and sugar, so make sure to use pumpkin puree.
- How to Tell if Muffins are Done: You can tell if the muffins are done by inserting a toothpick into the center of a muffin. If the toothpick comes out clean, the muffins are done.
- Don’t Over-Mix: Combine the wet ingredients and dry ingredients, but don’t over-mix the batter.
- Make your own Pumpkin Pie Spice: If you don’t have any pumpkin pie spice on hand you can make your own! Simply combine 1 and 1/4 teaspoons of cinnamon, 1/4 teaspoon of ground ginger, 1/4 teaspoon of nutmeg, and 1/4 teaspoon of allspice or ground cloves.
- Batter Consistency: If you are using a sugar-free sweetener, keep in mind that the batter may be thicker as they tend to absorb more liquid. If this is the case, add a splash of your milk of choice to the batter.
Serving Suggestions
Enjoy these pumpkin spice muffins for breakfast, dessert, or as a snack! You can even spread almond butter, peanut butter, or pumpkin butter on them. Or, enjoy these muffins with a cup of coffee, a homemade chai latte, or a pumpkin chai latte for a cozy fall treat!
Storage Instructions
You can store these muffins on the counter, in the refrigerator, and in the freezer. You can store these pumpkin muffins on the counter at room temperature for 1-2 days in an airtight container. Or, store them in an airtight container in the refrigerator for 3-4 days. Also, you can freeze these muffins in freezer-safe containers such as stasher bags for 2-3 months.
Healthy Pumpkin Spice Muffins FAQs
Are Pumpkin Spice Muffins Healthy?
These pumpkin spice muffins are a healthier option. They’re made with unsweetened applesauce, pumpkin puree, flour, eggs, and spices. There’s no butter or oil in this muffin recipe!
Can I Make Pumpkin Spice Muffins Gluten-Free?
Yes, you can make these pumpkin spice muffins gluten-free. Swap the all-purpose flour for a 1:1 all-purpose gluten-free flour.
Can You Freeze Pumpkin Spice Muffins?
Yes, you can freeze these pumpkin muffins. They will last 2-3 months in the freezer in a freezer-safe container.
More Healthy Muffin Recipes to Try!
Breakfast
Easy Apple Cinnamon Muffins
Breakfast
Healthy Banana Apple Muffins
Breakfast
Healthy Cranberry Orange Muffins
If you try this recipe please be sure to leave us a comment and star rating, ★★★★★, letting us know how it turns out for you.
Healthy Pumpkin Spice Muffins

Ingredients
- 1 ¾ cups all-purpose flour
- 1 ½ teaspoons baking soda
- 2 teaspoons pumpkin pie spice
- 3/4 cup brown sugar or Swerve brown sugar
- 2 eggs, whisked
- 1 teaspoon vanilla extract
- 1/4 cup unsweetened applesauce
- 15 ounce can pumpkin puree
Instructions
- Add the flour, baking soda, pumpkin pie spice, and brown sugar or Swerve brown sugar to a large bowl. Then, mix these ingredients.
- Add the whisked eggs, vanilla extract, unsweetened applesauce, and pumpkin puree to the bowl. Thoroughly combine all the ingredients but don’t over-mix the batter. *Sugar-substitutes tend to absorb more liquid, so if the batter is too dry, add a splash of milk and mix.
- Lightly spray a non-stick muffin pan with oil or use muffin liners. Pour the muffin batter into the muffin pan to make about 12 muffins. Bake the muffins at 350°F for 25-30 minutes, or until done, and enjoy!
Video

Notes
- Storage: Store leftover pumpkin spice muffins in an airtight container in the fridge for 3-4 days.
- Pumpkin Pie Spice: If you don’t have pumpkin pie spice, use 1 ¼ teaspoons ground cinnamon, ¼ teaspoon ground ginger, ¼ teaspoon ground nutmeg, and ¼ teaspoon ground allspice or cloves
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.





















Another great recipe! I was craving something warm and fall-esque even in the summer heat and these were perfect. I did make a couple substitutions. I didn’t have apple sauce so I just substituted it with greek yogurt for some added protein and cut down the sweetener to a little less than 1/2 cup (just personal preference for things a little less sweet). I also did 1 tsp baking soda and 1 tsp of baking powder to get a puffier, “bakery”-style domed muffin top. My family finished the batch in 2 days. I will be making these again! Perfect for a low calorie, sweet treat.
Thank you so much for sharing this! I love all of your substitutions and adjustments, especially the Greek yogurt and the bakery-style muffin tops! I’m so glad they turned out well and that your whole family enjoyed them. It sounds like you made them perfectly suited to your preferences. Thank you for giving the recipe a try, and I’m excited to hear you’ll be making them again!
Easy, healthy and delicious.
Hi Miyuki, I’m so happy you enjoyed these healthy pumpkin spice muffins, thanks so much for letting us know! 🙂
These are delicious!!! I didn’t have applesauce so I used a small mashed banana instead. To combat the overwhelming banana flavor I added some cinnamon! Legit the texture, the sweetness and flavor is amazing! MUST TRY!!
Hi Cindy, I’m so happy you loved the pumpkin spice muffins! Using mashed banana instead of applesauce was such a great idea, and I love that you added extra cinnamon. Thank you so much for sharing your tip, I’m sure others will find it super helpful too!
Omg these healthy pumpkin spice muffins were AMAZING! I just made these yesterday and they were so soft and fluffy and had the perfect pumpkin spice flavor. I love that there’s no oil or butter! Thanks for the great recipe, my whole family loved these muffins
Hi Michelle, I’m so happy to hear that you and your whole family loved these healthy pumpkin spice muffins! Thank you so much for leaving a review!
Loved this recipe!
Hi Bonnie, I’m so happy you loved the pumpkin spice muffins, thanks so much for leaving a review!
These healthy pumpkin spice muffins are moist, flavorful, and packed with cozy fall spices. Made with pumpkin purée and warm pumpkin pie spice, they’re the perfect easy recipe for autumn baking and meal prep.
Only have 1 egg?
No, this recipe calls for 2 eggs, which will be whisked before adding to the bowl. I’m sorry for any confusion!