Delicious light and soft Skinny Pumpkin Muffins made with whole grains, low in sugar and only 160 calories each. This is the BEST healthy pumpkin muffins recipe that yields muffins that actually taste like the bakery’s!

Healthy pumpkin muffins with chocolate chips, on a white plate.

These Skinny Pumpkin Muffins will not disappoint! They are soft and cake-like and the pumpkin spice flavors are delicious. I love that they’re healthier than most muffins, so we can all indulge in a little treat without feeling guilty. You can make them with or without chocolate chips, and they freeze really well so make a double batch to have on hand as a special snack.

How to make Pumpkin Muffins:

Start by mixing the dry ingredients together: flour, cornstarch, pumpkin spice, baking soda, baking powder, and salt.  If you don’t have pumpkin spice you can make your own by combining cinnamon, nutmeg, allspice and ginger.

Next, mix the eggs, honey, butter, and canned pumpkin in a separate bowl.

A clear glass mixing bowl with the batter for pumpkin muffins next to a muffin tin with the batter divided into the cups and chocolate chips on top.

Make a well in the center of the dry ingredients and pour the wet mixture in.  Stir the batter together, being careful not to over-mix it.  Now you can stir in some chocolate chips, if you’d like. Fill your muffin tin 2/3 full–this recipe makes 12 muffins.

Bake the muffins at 350 degrees for about 15-20 minutes.

A muffin tin with baked pumpkin muffins with chocolate chips.

What makes these pumpkin muffins healthy?

All right, I think we can all agree that there are healthier food options out there :).  But, as far as pumpkin bread goes, this recipe uses whole grains (yay for extra fiber), it has half the sugar, and a lot less butter or oil than traditional pumpkin bread recipes.  The best part is, they seriously still taste FANTASTIC!

A wire cooling rack with healthy pumpkin muffins cooling on it.

How to Make a Cake Flour Substitute:

You will notice that this recipe calls for cornstarch to be mixed with the whole wheat flour.  I added cornstarch to this recipe to make the flour more like cake-flour, which results in a more tender and soft muffin. If you don’t have cornstarch substitute more whole wheat flour.

The major difference between cake flour and purpose flour is in the protein content.  Cake flour is a more delicate type of flour that has a lower volume of protein.  Cooking with cake flour helps makes your bakery items, like these muffins, extra moist and tender.  I personally don’t usually buy cake flour.  Instead, I like to make my own version of cake flour by combining all-purpose flour with cornstarch. (In this case I used whole wheat flour).

You can make cake flour easily by substituting 2 tablespoons out of one cup of flour, for cornstarch. I like to add my cornstarch to the bottom of the 1 cup measurer and then fill the rest up with all-purpose flour, to make an even cup.


Half of a pumpkin muffin with a hand grabbing the side of it.



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Healthy pumpkin muffins with chocolate chips, on a white plate.
Prep 14 mins
Cook 16 mins
Total 30 mins
Add to Meal Plan


  • 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
  • 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. .


These freeze very well! Recipe adapted from Fueling a Fit Fam


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

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Tag @TastesBetterFromScratch on Instagram with #TastesBetterFromScratch!

Recipe inspired by 100 Days of Real Food.


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


Have you tried this recipe?!

RATE and COMMENT below! I would love to hear your experience.

Skinny Pumpkin Chocolate Chip Muffins recipe from Tastes Better From Scratch. These muffins are AMAZING! You'd never guess they were healthy too!

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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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  1. 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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