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These Healthy Pumpkin Muffins are made with whole wheat flour, warm spices, pumpkin, and sweetened with maple syrup. They’re moist, flavorful, and a great breakfast or snack for fall!

What Makes This Healthy Pumpkin Muffin Recipe Unique
Whole Grains – these muffins are made with 100% whole grains. White whole wheat flour gives them a lighter flavor and texture, but you still get the benefits of the whole grains.
Naturally sweetened – Pure maple syrup replaces refined sugar. The maple flavor also pairs perfectly with the pumpkin and warm spices. If you’d rather use and equal amount of brown sugar you can.
Easy to make – My healthy pumpkin muffin recipe is so easy to make! I used two bowls for them, but you can easily just make them in a single bowl. Just be sure to combine the wet ingredients in the bowl first before adding in the dry ones.

Ingredients you’ll need
- White whole wheat flour – White whole wheat flour is still 100% whole wheat. It’s not a combination of white and whole wheat and it’s not bleached. It’s mild in flavor and lighter in color than traditional whole wheat. All-purpose flour or a combination of all-purpose and whole wheat flour can be used as a substitution.
- Pumpkin pie spice – Use store bought or make a homemade blend.
- Cinnamon – While there is cinnamon in pumpkin pie spice already, I like to add additional to drive home that warm sweet flavor.
- Baking soda – Baking soda is a leavener that makes the muffins rise and gives them that gorgeous domed top.
- Salt – Diamond kosher salt is my go-to for both baking and cooking. Table salt has a saltier taste compared to kosher salt and sea salt so it may affect the flavor of the muffins.
- Pumpkin purée – Not to be confused with pumpkin pie filling which has added sugar. Libby’s is my go-to brand that I use.
- Maple syrup – Be sure to use pure maple syrup and not pancake syrup, which has no maple in it.
- Avocado oil – I like to use avocado oil because it’s neutral in flavor. It can be pricey compared to other oils so as an alternative you can use a good quality canola oil, vegetable oil, or melted coconut oil.
- Eggs – Eggs bind the muffins and give them structure.
- Milk – Both dairy and non-dairy milk can be used. For dairy milk I generally use 2% low-fat and for non-dairy I like to use unsweetened vanilla almond milk. Just be sure it’s unsweetened.
- Vanilla – My preference is to use vanilla bean paste in baking recipes because the flavor is more pure and intense. Vanilla extract works too.
- Pepitas – also labeled as pumpkin seeds. Be sure to not buy salted for this recipe. It adds a nice crunch to the muffins and keeps the muffins nut-free. You can swap with chopped pecans or walnuts if you prefer.






Tips for Making Healthy Pumpkin Muffins
- Don’t omit the oil or replace it with applesauce or something without fat. The fat gives the muffins moisture and without it they’ll be dry.
- Don’t overmix the batter or the muffins will be tough instead of light and fluffy. I like to fold the batter just until you can no longer see streaks for flour.
- If you use liners for the muffins, I recommend parchment paper liners. They release the muffin easily and none of it gets stuck. You can also grease the muffin tin instead of using liners.
- Add different mix-ins. Chocolate chips (You could also make these pumpkin chocolate chip muffins), raisins, pecans, or dried cranberries are a few of my favorites.
- If you like pumpkin muffins with streusel topping, make my pumpkin blueberry muffins or use the topping and add it to these muffins. It uses rolled oats and is so buttery and delicious!
- Let the muffins cool for at least 15 minutes before eating them. The cinnamon and pumpkin spice flavors will be bolder and more noticeable once they’ve cooled.

Storage and Freezing
I always think muffins taste best the day they are made, however these will keep for 2-3 days on the countertop or refrigerator in an airtight container.
To store them in the freezer, first let them cool to room temperature. Wrap them individually in plastic wrap and then put them in a resealable freezer bag. You can also flash freeze them on a sheet pan for about 30-60 minutes and then transfer them into an airtight container. The muffins will keep in the freezer for up to 3 months.

Healthy Pumpkin Muffin Recipe

Ingredients
Wet Ingredients
- 1/4 cup avocado oil, melted coconut oil or canola oil
- 1/2 cup maple syrup
- 2 eggs
- 1 cup pumpkin purée
- 1/4 cup milk of choice I used 2% low fat milk
- 2 teaspoons vanilla extract
Dry Ingredients
- 1 3/4 cup white whole wheat flour
- 1 teaspoon baking soda
- 1/2 teaspoon kosher salt
- 2 teaspoons pumpkin pie spice
- 1 teaspoon ground cinnamon
- 3 tablespoons unsalted pepitas, plus extra for sprinkling on top
Instructions
- Preheat oven to 350° F. and spray a 12-cup muffin pan with cooking spray or add muffin liners to it.
- In a large bowl whisk together the dry ingredients. In a smaller bowl whisk together the wet ingredients. Pour the wet in with the dry and stir them together with a rubber spatula until you no longer see streaks of flour. Don't over-mix.
- Stir the pepitas into the batter and then divide it evenly into the muffin pan. Place on the middle rack of the oven and bake for 15-20 minutes or until a toothpick inserted in the center of a muffin comes out clean or with a few crumbs attached.
- Let the muffins cool in the pan for 5-10 minutes before removing them onto a wire cooling rack.
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Tips for the best muffins
- Use a spoon to scoop the flour into the measuring cups. Don’t pack the flour in or you’ll have too much. Level the flour off with the back of a knife.
- Gently stir the muffin batter with a rubber spatula. Don’t beat or whip it. This will activate the gluten in the flour and cause your muffins to turn out tough.
- Bake the muffins on the middle rack of the oven. Baking on the top or bottom may result in the tops or bottoms of the muffins browning too much or burning.
More muffins you’ll love
- Cranberry Apple Carrot Muffins
- Cranberry Orange Muffins
- Pumpkin Apple Muffins
- Mini Chai Muffins with Vanilla Bean Glaze
- Lemon Zucchini Muffins
If you make these Healthy Pumpkin Muffins, please leave a comment and/or give this recipe a rating! I love hearing from you and do my best to respond to your comments. And if you’re on Instagram tag @reciperunner so I can see your beautiful creations!











