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!
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It’s officially that time of year! Pumpkin season is in full effect and these Whole Wheat Pumpkin Muffins have been on repeat. Perfectly soft and moist, this pumpkin muffin recipe makes the perfect cozy treat for your family this weekend. The best part about these healthy pumpkin muffins are that you can easily throw them together in just 30 minutes and are made healthier with whole wheat flour, applesauce and zero butter or refined sugar. These pumpkin muffins are perfect for a quick breakfast, healthy snack or treat alongside your morning coffee!
Why You’ll Love these Muffins
- Wholesome ingredients – made with whole wheat flour and naturally sweetened with applesauce and maple syrup with no added sugar.
- Perfectly moist – applesauce, pumpkin purée and a little coconut oil make these muffins deliciously moist and fluffy!
- Customizable – this delicious recipe is easily customizable with fun mix-ins like chocolate chips, chopped nuts, shredded coconut, dried fruit or fresh berries.
- Freezer-friendly – bake once or make a double batch to enjoy all season long! Definitely one of our favorite recipes with tons of fall flavor.
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 regular whole wheat flour, white whole wheat flour or 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.
- sweeteners – I used a combination of pure maple syrup and cane sugar to sweeten these muffins without using any refined sugar, but you could also use honey, brown sugar 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. You could also make your own pumpkin pie spice using nutmeg, ginger, allspice and cloves.
How to Make Pumpkin Muffins
- Mix ingredients. In a large mixing bowl, whisk together the flours, baking powder, baking soda, pumpkin pie spice, cinnamon and salt, then set aside flour mixture. 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 muffin 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 muffin liners) and divide the batter evenly between 12 muffin cups, making sure to fill each cup almost all the way full.
- Bake the muffins. Bake the muffin tin 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.
Tips for Making the BEST Pumpkin Muffins
- Make sure you DON’T over mix the batter. This results in super dense muffins which we don’t want. We are going for fluffy and soft!
- Feel free to sub the whole wheat pastry flour with 1:1 gluten-free flour or even all-purpose flour. I don’t recommend using almond flour or coconut flour in this recipe.
- Mix in other fun additions like chopped walnuts or pecans, coconut flakes, dried fruit, fresh berries or a whole cup of chocolate chips!
- To make these pumpkin muffins vegan, use flax eggs in place of the regular eggs and use vegan cream cheese for the glaze.
- This recipe also makes 24 mini muffins. Distribute the batter into 24 muffins cups and bake for 15 to 17 minutes. Perfect treat for little hands!
- If you love this recipe, make sure to try our delicious healthy pumpkin bread recipe!
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 healthy 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 a large freezer bag. When ready to eat, just pop them in the microwave for 30 to 40 seconds or simply thaw out at room temperature. These will keep in the freezer for up to 3 months!
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More Pumpkin Recipes
- Healthier Pumpkin Bars
- Healthy Pumpkin Zucchini Bread
- Gluten-Free Pumpkin Spice Donuts
- Almond Flour Pumpkin Bread
- Fluffy Pumpkin Pancakes
- Pumpkin Spice Mug Cake
More Muffin Recipes
- Healthy Apple Cinnamon Muffins
- Chocolate Chip Banana Zucchini Muffins
- Lemon Blueberry Blender Muffins
- Strawberry Jam Filled Oat Muffins
- Banana Breakfast Muffins
Hope you all enjoy these Whole Wheat Pumpkin Muffins! If you love this dessert as much as we do, please leave me 
below and don’t forget to tag me on Instagram using the hashtag #eatyourselfskinny! I love seeing all your delicious recreations!
Whole Wheat Pumpkin Muffins
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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
Instructions
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Preheat oven to 350 degrees F.
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In a small bowl, whisk together flours, baking powder, baking soda, cinnamon, pumpkin pie spice and salt; set aside.
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In a separate bowl, whisk together eggs, pumpkin, maple syrup, cane sugar, applesauce, coconut oil, and vanilla until all combined. Add wet ingredients into flour mixture and mix with a spatula until just combined, being careful not to over-mix.
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Divide batter evenly between 12 muffin cups sprayed with non-stick cooking spray (or you can use paper liners) making sure to fill each cup almost all the way full.
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Bake the muffins in the oven for 20 to 25 minutes, or until a toothpick inserted comes out clean, then let the muffins cool in the pan for 5 minutes before transferring them to a wire rack.
Nutrition
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