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These Healthy Pumpkin Muffins are soft, fluffy, perfectly spiced, and packed with cozy fall flavor. Made with pumpkin puree, ripe banana, whole-wheat flour, and just a touch of maple syrup, they’re naturally moist, lightly sweet, and easy enough to whip up anytime you need a quick breakfast or snack.
Featured Reader Comments
“5 stars!! Delicious recipe and love that these are healthy! Great fall snack for my family and I!” -Beth
“I used all whole wheat flour and replaced the butter with olive oil. They are delicious!” -Liz
Healthy Pumpkin Banana Muffins
I started making these healthy pumpkin muffins more than a decade ago with a simple goal in mind: to create a wholesome mid-afternoon snack that I could make in bulk and stash away in the freezer for busy days.
These healthy pumpkin muffins are soft, fluffy, perfectly spiced, and made with ingredients you can feel good about – yes, actually. Pumpkin puree and ripe banana keep them naturally moist and add plenty of flavor, while whole wheat flour, ground flaxseed, and chia seeds give them a little extra lasting energy. They’re lightly sweetened with maple syrup, easy to make in one bowl, and perfect for breakfast, lunchboxes, or an afternoon snack.
Basically, all the cozy pumpkin muffin goodness – just a little more wholesome.
Table of Contents
Ingredients and Substitutions
Below you’ll find notes for the ingredients that need a little extra explanation. You can find the complete ingredient list with measurements in the recipe card below.
- Flour: These muffins are made with a combination of all-purpose flour and whole wheat flour. The all-purpose flour keeps the muffins soft and fluffy, while the whole wheat flour adds a little more whole-grain goodness without making them too dense. If you prefer, you can use all whole wheat flour, although the muffins may be slightly denser. In this case, try adding 2 to 3 extra tablespoons of milk or using whole wheat pastry flour instead.
- Ground flaxseed and chia seeds: I love adding a flax and chia seed blend for a little extra fiber and texture. If you don’t have a blend, ground flaxseed or chia seeds can be used on their own.
- Pumpkin puree: Be sure to use pure pumpkin puree, not pumpkin pie filling. Homemade pumpkin puree also works, or puree some leftover sweet potato or butternut squash for a near identical flavor and texture. Learn how to cook pumpkin here.
- Ripe banana: The riper, the better. Banana adds natural sweetness and moisture, allowing these muffins to use much less added sweetener than a traditional muffin recipe.
- Maple syrup: Just three tablespoons lightly sweeten the entire batch. Honey may be substituted if preferred.
- Milk: Any dairy or unsweetened plant-based milk will work, including almond, oat, or soy milk.
- Eggs: Acts as a binding agent, providing structure and moisture to the muffins. Possible substitutions include a flax or chia “egg.” Combine 1 tablespoon of ground flax or chia seeds with 3 tablespoons of water and let it sit until it thickens (equivalent to 1 egg). Unsweetened applesauce is another fantastic egg substitute. You’ll need ¼ cup of applesauce for 1 egg.
- Coconut oil or butter: Either works well and adds richness and moisture. Melt whichever one you’re using before mixing it with the wet ingredients.
- Cinnamon: Ground cinnamon gives the muffins their warm, cozy flavor. You can substitute pumpkin pie spice for even more fall spice.
- Optional nuts: Chopped pecans or walnuts add a little crunch, but they’re completely optional. Chocolate chips are also delicious if you want a sweeter muffin.
How to Make Healthy Pumpkin Muffins
These healthy pumpkin muffins come together quickly using the classic muffin method: mix the dry ingredients in one bowl and the wet ingredients in another, then gently combine the two.
The most important part is not to overmix the batter. Fold everything together just until you no longer see streaks of dry flour. A few small lumps are perfectly fine and will help keep the muffins soft and fluffy rather than dense.
Divide the batter between a prepared muffin pan and bake at 350°F until the tops are set and a toothpick inserted into the center comes out clean. Let the muffins cool briefly in the pan before transferring them to a wire rack.
They’re delicious warm with a little butter, but they’re just as good once cooled – especially for breakfast, lunchboxes, or an easy grab-and-go snack.
Jessica’s Tips for the Best Pumpkin Muffins
- Don’t overmix the batter: Once you add the dry ingredients to the wet ingredients, mix just until combined. Overmixing can make the muffins dense instead of soft and fluffy.
- Use a very ripe banana: A ripe, spotty banana adds more natural sweetness and moisture, which is especially important since these muffins contain very little added sweetener.
- Make mini muffins: This recipe works great as mini muffins. Fill a greased mini muffin pan about 3/4 full and bake at 350°F for approximately 12-15 minutes, or until a toothpick inserted into the center comes out clean.
- Add your favorite mix-ins: Try chocolate chips, shredded coconut, chopped walnuts, or pecans. Keep additions moderate so the batter isn’t weighed down.
- Add a streusel topping: For a sweeter, more bakery-style muffin, combine 1/2 cup rolled oats, 1/4 cup flour, 1/4 cup brown sugar, a pinch of cinnamon, and about 3 tablespoons melted butter or coconut oil. Sprinkle over the muffin batter before baking.
Storage and Freezing
- To store: Allow the muffins to cool completely, then transfer them to an airtight container. Store at room temperature for up to 2 days or in the refrigerator for up to 5 days.
- To freeze: Place the cooled muffins in a freezer-safe bag or container and freeze for up to 3 months. For best results, wrap them individually before freezing so you can grab one at a time.
- To reheat: Thaw overnight in the refrigerator or at room temperature, then warm briefly in the microwave if desired.
More Pumpkin Recipes
If you make this healthy pumpkin muffins recipe, I would love to hear how it turned out in the comment section below! Your review will help other readers in the community. And if you’re hungry for more delicious food inspiration and exclusive content, join my free newsletter here.
Healthy Pumpkin Muffins Recipe
Ingredients
- 1 cup all-purpose flour
- ½ cup whole wheat flour
- 3 tablespoons ground flaxseed/chia seed blend
- ¾ teaspoon baking soda
- ¾ teaspoon baking powder
- ¼ teaspoon salt
- 1 teaspoon ground cinnamon, or pumpkin pie spice
- 2 large eggs, at room temperature
- ½ cup milk, any kind you prefer
- 3 tablespoons maple syrup, or honey
- 3 tablespoons coconut oil, or butter, melted
- 1 teaspoon vanilla extract
- ½ cup pumpkin puree, not pumpkin pie spice
- 1 large ripe banana, mashed
- ¾ cup chopped pecans or walnuts, optional
Instructions
- Preheat the oven to 350°F (175°C). Lightly spray a muffin tray with non-stick cooking spray or line with muffin liners. Set aside.
- Prepare the dry ingredients: In a medium-sized mixing bowl, whisk together the all-purpose flour, whole wheat flour, ground flax/chia seed blend, baking soda, baking powder, salt, and ground cinnamon. Set aside.1 cup all-purpose flour, ½ cup whole wheat flour, 3 tablespoons ground flaxseed/chia seed blend, ¾ teaspoon baking soda, ¾ teaspoon baking powder, ¼ teaspoon salt, 1 teaspoon ground cinnamon
- Combine the wet ingredients: In a separate large mixing bowl, whisk together the eggs, milk, maple syrup, melted butter or coconut oil, vanilla extract, pumpkin puree, and mashed banana until smooth.2 large eggs, ½ cup milk, 3 tablespoons maple syrup, 3 tablespoons coconut oil, 1 teaspoon vanilla extract, ½ cup pumpkin puree, 1 large ripe banana
- Mix the dry ingredients with the wet: Gently fold the dry ingredients into the wet ingredients, being careful not to overmix. If desired, fold in the chopped nuts.¾ cup chopped pecans or walnuts
- Fill the muffin tray: Divide the batter evenly between 12 prepared muffin cups. If desired, sprinkle the tops with additional chopped nuts or rolled.
- Bake: Place the tray in the oven and bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean.
- Cool and serve: Let the muffins cool in the tray for 5 minutes before transferring to a wire rack to cool completely. Enjoy!
Notes
- To make this recipe with homemade pumpkin puree, you’ll need approximately 1 3/4 cups.
- Store leftovers in an airtight container in the fridge for up to 5 days.
- To freeze, cool completely then wrap each muffin individually in plastic wrap, and place them in a large ziplock freezer bag. Store in the freezer for up to 3 months. To enjoy, remove from the freezer, unwrap, and microwave for 30 seconds or until warm.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
My muffins stick to the liners. Otherwise; these were delicious! What did I do wrong?
Hi Crystal,
I am glad you found these delicious.
This does happen with some muffin pan liners. To prevent this next time with the same liners, try spraying the liners with non-stick spray. 🙂
We added almonds & semi-sweet choc chips! Used coconut oil. Yummy!!!!!! 5 ⭐️ Stars
I used all white flour (it was all I had at the time) and Walden Farms syrup to cut out all the sugar, and they turned out great! I mixed some monk fruit and cinnamon and sprinkled on top prior to baking to give it a cinnamon sugar taste on top. Everyone who tried then loved them! Definitely keeping this recipe in my rotation. Thanks!
I used all whole wheat flour and replaced the butter with olive oil. They are delicious!
5 stars!! Delicious recipe and love that these are healthy! Great Fall snack for my family and I! <3
Hello!
Can you use all whole wheat flour instead of the combination of the two flours?
Hi Marne,
That is a good question! While I have not tried that personally, I don’t see why using only whole wheat flour would not work. If you try it, please do report back!