This Healthy Pumpkin Muffins recipe is made with whole grains, less butter and sugar, and only 160 calories each! They taste just like the bakery and are freezer friendly!

Looking for more pumpkin recipes? Try my Pumpkin Chocolate Chip Bread, Classic Pumpkin Roll, or Pumpkin French Toast!

Healthy pumpkin muffins on a cooling rack, with a bite taken from one.

What I love about them:

  • Healthy, but just as good as a bakery – I love that these have less sugar and fat than regular pumpkin muffins, but they still taste like a sweet treat and I can feel comfortable offering them to my kids.
  • Freezer Friendly – Make a double batch and freeze the leftovers for a quick snack, or for part of kids lunches.

How to make Healthy Pumpkin Muffins:

Combine dry ingredients: flour, cornstarch, pumpkin spice, baking soda, baking powder, and salt. 

Dry ingredients stirred together in a mixing bowl.

Mix wet ingredients in a separate bowl: eggs, honey, butter, and canned pumpkin puree (or homemade pumpkin puree). Make a well in the center of the dry ingredients and pour the wet mixture in. 

Canned pumpkin, eggs, honey, melted butter stirred together in a mixing bowl.

Stir batter together, being careful not to over-mix it, and then add chocolate chips (optional). Divide batter between the muffin cups.

Pumpkin muffin batter stirred together in a bowl.

Bake muffins at 350 degrees F for about 15-20 minutes. Enjoy!

Freshly baked, healthy pumpkin muffins in a muffin tin.

My Secret Ingredient:

I wanted to make these muffins healthier, but when using all whole wheat flour, baked goods often turn out dense. I decided to incorporate a little cornstarch as a secret ingredient that helps the flour act more like cake flour, which has a lower protein content and makes bakery items extra tender. If you don’t have cornstarch, substitute ¼ cup more whole wheat flour.

Freezing Instructions:

To Freeze: Allow muffins to cool completely, then place them in a freezer safe container and store them in the freezer for up to 3 months. 

More Healthy Muffin Recipes:

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Healthy pumpkin muffins on a cooling rack, with a bite taken from one.
Prep 14 mins
Cook 16 mins
Total 30 mins
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  • 1 1/4 cups whole-wheat flour
  • 1/4 cup cornstarch
  • 1 Tablespoon pumpkin pie spice
  • 1 teaspoon baking soda
  • ¼ teaspoon baking powder
  • ½ teaspoon salt
  • 2 large eggs
  • 1/2 cup honey
  • 1/3 cup melted butter , or coconut butter
  • 1 cup canned pumpkin puree
  • 1/2 cup semi-sweet chocolate chips , optional


  • Preheat the oven to 350 degrees F. Spray a standard 12-cup muffin tin with non-stick cooking spray (or line with muffin liners).
  • Whisk dry ingredients together: flour, cornstarch, pumpkin spice, baking soda, baking powder, and salt.
  • Mix wet ingredients together: eggs, melted butter, honey, and pumpkin puree.
  • Make a well in the center of the flour mixture and add the pumpkin mixture and chocolate chips. Mix just until combined. (Do not over-mix).
  • Spoon the batter into the muffin pan, filling each cup 2/3 full (or a little more if you want bigger muffins). Bake for 16 – 18 minutes or until a toothpick inserted comes out clean. .


Freezing Instructions:Allow muffins to cool completely, then place them in a freezer safe container and store them in the freezer for up to 3 months.


Calories: 161kcalCarbohydrates: 25gProtein: 3gFat: 6gSaturated Fat: 3gCholesterol: 44mgSodium: 247mgPotassium: 118mgFiber: 2gSugar: 12gVitamin A: 3380IUVitamin C: 1.1mgCalcium: 24mgIron: 1mg

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Recipe inspired by 100 Days of Real Food.

I originally shared this recipe October 2015. Updated September 2018 and October 2021.

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About The Author

Lauren Allen

Welcome! I’m Lauren, a mom of four and lover of good food. Here you’ll find easy recipes and weeknight meal ideas made with real ingredients, with step-by-step photos and videos.

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Recipe Rating


  1. Made these with AP flour, they were super good but were a bit dry. Any recommendations on how to make these more moist?


  2. 5 stars
    I have now brought this dessert to back-to-back friend gatherings and it was a hit at both! It is so easy to make and is honestly the best apple crisp I have had. Served with a scoop of vanilla ice cream…yum!!

  3. 5 stars
    One of my girlfriends recently brought these to a get together and they were the first thing gone. Everyone was asking for the recipe and she shared that she got the recipe from your site. I will definitely be making these soon – they were amazing!

  4. 5 stars
    I made this today with my Kindergarten class. We had to make some changes due to allergies. We used flax eggs and applesauce instead of melted butter. They turned out so moist and delicious! And completely vegan!

  5. 5 stars
    These came out so moist and delicious! I didn’t have any chocolate chips on hand so added a bit of cream cheese extract instead to add a little extra kick. I’ll definitely be making these again, hopefully with chocolate chips!

  6. 3 stars
    I was looking for a pumpkin muffin recipe with whole wheat flour. This one intrigued me but I agree with what other reviews said-the texture was gritty. Sorry.

  7. I was wondering if I could substitute banana for the pumpkin, keeping everything else the same? They sound delicious with the pumpkin, but I have some bananas I need to use up. These really look wonderful.

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