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 Chocolate Chip Muffins on a platter with a bite taken out of the front 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.
  • Add protein: Make them even healthier by replacing a few tablespoons of the flour with a scoop of protein powder!

How to make Healthy Pumpkin Muffins:

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

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 then pour the wet mixture in. 

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

Three images showing the dry ingredients, wet ingredients, and after they are combined to make a pumpkin muffin batter.

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

Freshly baked, healthy pumpkin muffins in a muffin tin.

Freezing Instructions:

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

More Healthy Muffin Recipes:

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Healthy Pumpkin Chocolate Chip Muffins on a platter with a bite taken out of the front one.
Prep 14 minutes
Cook 16 minutes
Total 30 minutes
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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. .


Cornstarch 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: Allow muffins to cool completely, then store in a freezer safe container and freeze 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, October 2021 and September 2023.

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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. 5 stars
    I was not sure if I would like whole wheat flour. At first was not sure but kept coming back for another one. My husband likes them also. I made two batches so far! Thank you.


  2. 4 stars
    I altered the recipe a bit so gave it 4 stars because of this. I used half agave and half brown sugar with the same measurements as honey. I also used vegetable oil in place of butter and added a 1/4 cup of unsweetened applesauce as I felt the ingredients would yield a drier muffin if it didn’t have added moisture. I also used half AP flour and half whole wheat. Half cup of mini choc chips. The result was a delicious 5 star muffin.

  3. What kind of whole wheat flour did you use in these muffins? I have hard white wheat and soft white wheat and wasn’t sure which one would be best to use for this recipe. Thank you!

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