Name: Whole Wheat Pumpkin Muffins
Prep time: 10 min
Cook time: 20 min
Total time: 30 min
Ingredients: 1 cup whole wheat pastry flour; 1/2 cup all-purpose flour; 1 teaspoon baking powder; 1/2 teaspoon baking soda; 2 teaspoons cinnamon; 1 teaspoon pumpkin pie spice; 1/2 teaspoons salt; 2 eggs; 1 cup 100% pure pumpkin (not pumpkin pie filling); 1/2 cup maple syrup; 1/4 cup cane sugar; 2 tablespoons applesauce; 1/4 cup coconut oil, melted and cooled; 1 teaspoon vanilla

Whole Wheat Pumpkin Muffins

Jump to Recipe

These Whole Wheat Pumpkin Muffins are moist, fluffy, and made healthier with whole wheat flour, applesauce, and zero butter or refined sugar. Loaded with delicious pumpkin flavor and warm spices for the perfect fall muffin!

Is it even fall if you don’t make delicious pumpkin muffins on repeat?? These muffins are perfectly fluffy, loaded with so much warm pumpkin flavor, and make the perfect cozy treat for your family this weekend. The best part about these whole wheat pumpkin muffins are easily made in just 30 minutes and made healthier with whole wheat flour, applesauce and zero butter or refined sugar!

Why You’ll Love these Muffins

Pumpkin, maple syrup, vanilla and warm spices make this the perfect fall treat!
Made with whole grains, applesauce and zero butter or refined sugar.
Easily customizable with fun mix-ins like chocolate chips, chopped nuts, shredded coconut, dried fruit or fresh berries.
Can easily make this into pumpkin bread or bite-sized, poppable mini muffins for tiny hands.
Freezer-friendly so enjoy these all season long!

Ingredients You’ll Need

whole wheat pastry flour – I love baking with whole wheat pastry flour as it has all the nutritional benefits of whole grain flour while making these muffins light and fluffy. I highly recommend using this, but if you don’t have any on hand you could use white whole wheat flour or regular all-purpose flour
all-purpose flour – when mixed with the whole wheat flour, this helps makes these muffins even softer and fluffier, but feel free to use all whole wheat pastry flour if you prefer.
baking powder + baking soda – acts as a leavening agent to help these muffins rise.
pumpkin puree – I used canned pumpkin purée for this, just make sure you use 100% pure pumpkin and not pumpkin pie filling as that is loaded with tons of sugar.
eggs – adds protein and gives these muffins their structure and height.
sweetener – I used a combination of maple syrup and cane sugar to sweeten these muffins without using any refined sugar, but you could also use honey or even regular sugar.
coconut oil – for additional moisture and fluffiness! Feel free to sub with another type of oil if you prefer or even butter.
applesauce – this helps to reduce the amount of oil we need to use and helps keep the muffins moist. You could also use Greek yogurt or mashed banana as well.
warm flavors – a delicious combination of pumpkin pie spice, cinnamon, salt and vanilla extract.

How to Make Pumpkin Muffins

Mix ingredients. In a large bowl, whisk together the flours, baking powder, baking soda, pumpkin pie spice, cinnamon and salt, then set aside. In a medium bowl, stir together the eggs, maple syrup, cane sugar, pumpkin puree, applesauce, melted coconut oil, and vanilla, mixing until all combined.
Make the batter. Add the dry ingredients to the wet ingredients and mix with a spatula until just combined, being careful not to over-mix the batter. This is when you can fold in any mix-ins you’d like such as chocolate chips or chopped nuts. Generously coat a muffin pan with non-stick cooking spray (or use paper liners) and divide the batter evenly between 12 muffin cups, making sure to fill each cup almost all the way full.
BAKE! Bake the muffins in the oven at 350 degrees F for 20 to 25 minutes (mine came out perfect at 22 minutes), or until a toothpick inserted comes out clean. Let the muffins cool in the pan for about 5 minutes before transferring them to a wire rack.

Prepping and Storage

To Store: You can keep these muffins stored in a sealed, airtight container or wrapped in aluminum foil on the counter at room temp for up to a day, but make sure to refrigerate after that to keep them longer. These muffins will last up to a week in the fridge in a sealed container.

To Freeze: These muffins freeze really well too! You can either wrap the muffins individually in plastic wrap or store them all together in freezer-safe bags. When ready to eat, just pop them in the microwave for 3o to 40 seconds or simply thaw out at room temperature. These will keep in the freezer for up to 3 months!

More Pumpkin Recipes You’ll Love

More Muffin Recipes You’ll Love

Hope you all enjoy these Whole Wheat Pumpkin Muffins and if you love this recipe as much as we do, please leave me a five-star rating below and don’t forget to tag me on Instagram using the hashtag #eatyourselfskinny! I love seeing all your delicious recreations!

RECIPE