These Healthy Pumpkin Muffins are soft, fluffy and easy to make with gluten free flour, pure pumpkin and cozy warm spices. A one bowl muffin recipe and perfect for a quick grab-and-go fall breakfast or afternoon treat. Dairy-free, refined-sugar free, grain-free, gluten-free, paleo-friendly with low carb keto sweetener options.
Updated September 2021
Healthy Pumpkin Muffin Recipe
Looking for a delicious and healthy breakfast for on the go? These Healthy Pumpkin Muffins are super soft, tender, moist and come together in just ONE bowl! Made with gluten free wholesome ingredients, packed with pure pumpkin and cozy autumn spices. This easy muffin recipe is a paleo spin on our Keto Pumpkin Muffins and perfect for pumpkin lovers!
Autumn is our favorite baking season and my kids love all things pumpkin, especially once September and October come around. Other healthy pumpkin recipes we make often include this healthy Pumpkin Pie, Healthy Pumpkin Bread, Pumpkin Spice Latte and Pumpkin Cookies.
Why we love this delicious pumpkin muffin recipe
- This healthy pumpkin muffin recipe is so easy to make and comes together in just ONE bowl with NO mixer required.
- Made with wholesome grain-free, dairy-free, paleo and gluten-free ingredients that you can enjoy as a healthy breakfast, afternoon snack or after dinner dessert.
- Full of cozy warm spices and delicious pumpkin flavor.
- An easy and healthy pumpkin muffin recipe made with simple ingredients you most likely already have in your kitchen pantry.
Ingredients you need for Pumpkin Muffins
Most homemade pumpkin muffin recipes we saw used a combination of whole wheat flour, rolled oats, brown sugar, butter and milk. To keep these healthy pumpkin muffins gluten free and paleo-friendly, you’re going to need:
Wet Ingredients and sweetener:
- Eggs – binds the ingredients together and help the muffins rise. I have not tried using chia eggs or flax eggs to make these pumpkin muffins vegan but would love to hear if you do.
- Pumpkin puree: be sure to use pure sugar free canned pumpkin puree (not pumpkin pie filling) or homemade pumpkin puree. Be sure not to use canned pumpkin pie filling though since it’s packed with other sweeteners and fillers.
- Unsalted Drippy Almond Butter: You could also use cashew butter, sunflower seed butter or any other nut or seed butter, if preferred. If not paleo, peanut butter would be delicious too.
- Unsweetened almond milk – helps add moisture. You can use any dairy-free (or any) milk you like.
- Coconut sugar – An unrefined sugar that mimics the taste of brown sugar. You can sub with another granulated brown sugar sweetener / substitute of your choice such as golden monk fruit sweetener or brown Swerve to make these pumpkin muffins keto
- Coconut Oil – melted and cooled. Use refined if you’re not a fan of the coconut flavor. Any other neutral tasting oil, vegan butter, melted ghee or regular butter would work if not dairy-free.
- Pure vanilla extract – adds flavor, balances sweetness and makes these healthy pumpkin chocolate chip muffins delicious
- Baking powder and baking soda: this combination of leaveners help the paleo chocolate pumpkin muffins rise
- Super fine blanched almond flour: our favorite paleo, low carb gluten-free flour to use in place of all purpose flour
- Homemade pumpkin pie spice – you can use your favorite brand or make your own pumpkin spice with a combination of ground cinnamon, ground ginger, ground nutmeg, ground cloves and ground mace.
- Dairy-free chocolate chips
How to make Healthy Pumpkin Muffins from scratch
PREP MUFFIN PAN AND PREHEAT OVEN: Preheat the oven to 375ºF. Grease or line a 12 pan muffin tin with paper liners and grease with coconut oil (it’s important to grease them otherwise they will stick to the liners).
MIX THE WET INGREDIENTS: In a large bowl, beat the eggs until fluffy then add pumpkin puree, nut butter, coconut sugar, coconut oil, milk and vanilla. Mix well until fully combined.
ADD THE DRY INGREDIENTS: Stir in almond flour, pumpkin pie spice, baking soda and baking powder and mix until combined. Fold in chocolate chips.
DIVIDE BATTER: Divide the batter between the prepared muffin tins (I use a cookie scoop) and top with extra chocolate chips.
- BAKE: Bake in preheated oven for 17-21 minutes or until a toothpick inserted into the center of a muffin comes out clean.
- COOL: Remove pan from oven and allow the muffins to cool in pan for 10 minutes.
Tips for the Best Healthy Pumpkin Muffins
- Blot the pumpkin puree with a paper towel or cheesecloth: It’s important to remove any extra moisture from your pumpkin puree to prevent the muffins from getting soggy.
- Measure your flours correctly using the spoon and scoop method. Do NOT scoop directly from the bag.
- Line your muffin pan with liners: Be sure to use parchment paper liners or silicone muffin liners for easier removal and clean-up.
Want to switch up this amazing pumpkin recipe?
- Make a dairy-free or regular cream cheese filling with a mix of cream cheese, almond milk and your favorite low carb sweetener
- Top with a dairy-free or regular cream cheese frosting
- Add a gluten free streusel topping
- Bananas – Add in a mashed ripe banana in place of one of the eggs for delicious Pumpkin Banana Muffins
- Applesauce – you can make these Healthy Pumpkin Muffins with applesauce by replacing one of the eggs with 1/4 cup applesauce
- Hemp seeds or flaxseeds – add an additional crunch and bumps up the fiber and protein.
- Nuts. We love adding chopped walnuts or pecan
- Spread a dollop or a smear of nut butter, maple syrup or dairy-free cream cheese on your muffins for a delicious afternoon snack or after-dinner dessert
Frequently Asked Questions
Can this pumpkin muffin recipe be made into bread?
Yes, to make healthy pumpkin bread simply pour your batter into an 8×4 loaf pan. Or you can even divide the batter into mini loaf pans for mini bread loaves.
Are pumpkin muffins healthy for you?
Some low calorie pumpkin muffins recipes we saw use whole wheat pastry flour and other artificial sweeteners and flavors which we prefer not to include in our muffin recipes.
Our healthy pumpkin muffins with almond flour are not just delicious, they are also grain-free, gluten-free and refined-sugar free.
What makes these pumpkin muffins healthy?
- Unlike many low fat pumpkin muffins we saw, this one is made with wholesome grain-free and refined sugar-free ingredients.
- Instead of all purpose white flour, we use grain free almond flour
- Made with coconut oil instead of butter
- Sweetened with unrefined sugar instead of brown sugar.
Storage and Freezer Tips
To store your gluten free pumpkin muffins, keep them in an airtight plastic bag in the refrigerator. They’ll stay good for 3-4 days. You can eat them cold or reheat them in the microwave!
How to Freeze Pumpkin Muffins
The great thing about these paleo pumpkin muffins is that you can make them ahead of time since they freeze beautifully! You can make a double batch on your Sunday meal prep and then warm them up to enjoy them throughout the week.
Once the muffins are cooled, place them in a freezer bag and freeze for up to 3 months. Thaw at room temperature or in the microwave.
Recommended Tools You’ll Need For this Recipe:
What can you do with canned pumpkin
Try these healthy pumpkin recipes:
These Healthy Pumpkin Muffins are soft, fluffy and easy to make with grain-free flour, pure pumpkin and cozy warm spices. A one bowl muffin recipe and perfect for a quick grab-and-go fall breakfast or afternoon treat. Grain-free, gluten-free, paleo-friendly with low carb keto sweetener options.
- 3 large eggs , room temperature
- 1/4 cup drippy almond butter , sub with any creamy nut butter or seed butter
- 1/4 cup coconut oil , melted and cooled
- 3 tablespoons unsweetened almond milk
- 1 cup pure pumpkin puree NOT pumpkin pie filling
- 3/4 cup coconut sugar , sub golden monk fruit sweetener or brown sugar substitute for low carb / keto
- 1 1/2 teaspoons pure vanilla extract
- 1 1/3 cups superfine blanched almond flour
- 1 tablespoon pumpkin pie spice
- 1 teaspoon baking powder
- 3/4 teaspoon baking soda
- 1/3 cup dairy-free chocolate chips , (we use Pascha's, Hu's Gems or Lily's Sweets) plus more for topping if desired
PREP MUFFIN PAN AND PREHEAT OVEN: Preheat the oven to 375ºF. Grease or line a 12 pan muffin tin with parchment paper liners and grease with coconut oil (it's important to grease them otherwise they will stick to the liners).
MIX THE WET INGREDIENTS: In a large bowl, beat the eggs until fluffy then add the pumpkin puree, nut butter, coconut sugar, coconut oil, milk and vanilla. Mix well until fully combined.
ADD THE DRY INGREDIENTS: Stir in the almond flour, pumpkin pie spice, baking powder and baking soda and mix until combined. Fold in the chocolate chips.
DIVIDE BATTER: Divide the batter evenly between the prepared muffin tins (I use a large cookie scoop) and top with extra chocolate chips.
BAKE: Bake in preheated oven for 17-19 minutes or until a toothpick inserted into the center of a muffin comes out clean.
- Remove pan from oven and allow the muffins to cool in pan for 10 minutes.
NUTRITIONAL VALUE CALCULATED WITHOUT SUGAR FREE CHOCOLATE CHIPS AND NUTS.