These Healthy Pumpkin Muffins are low sugar, low fat and yet sweet and moist fall breakfast, afternoon snack or dessert. They are delicious and so easy to make!
This time of year, pumpkin banana muffins, almond flour pumpkin muffins and pumpkin chocolate chip muffins are among our favorite recipes to make.
Healthy pumpkin muffins is a delicious way to cheer you up while mourning the end of summer days yet at the same time welcoming busy days of fall. They fill any kitchen with warm delicious smells of autumn!
These fluffy muffins are a copycat of Starbucks pumpkin cream cheese muffins but with 2 times less sugar and fat, 1.5 times less calories and carbs, and 3 times more fiber!
Why You’ll Love This Recipe
- Low sugar and low fat: Starbucks pumpkin muffin contains 14 grams of fat and 34 grams of sugar. These muffins have only 7 grams of fat and 19 grams of sugar. Might seem high but that’s twice less, and muffin still has to taste good!
- Wholesome ingredients: Including whole grains and pure pumpkin puree which are an amazing source of vitamins, nutrients and fiber.
- Easy to make: Basic ingredients and no separate bowls – less mess, less stress!
- Freezer friendly: Make a batch now and freeze a few for later.
- Craving satisfied: Move over PSL, these are the best muffins with warm spices that hit the spot!
Ingredients for Healthy Pumpkin Muffins
- Canned pumpkin puree: You can use store-bought or homemade pumpkin puree. Just be sure not to buy pumpkin pie filling! Here is a quick tutorial how to roast pumpkin and make pumpkin puree.
- Eggs: 2 large eggs to bind the ingredients. I have not tried making these muffins vegan, but you can try to substitute eggs with flax eggs.
- Any oil: A neutral oil such as avocado oil, light olive oil or melted coconut oil.
- Maple syrup or honey: Any liquid sweetener works. Please do not use any dry sugar like white sugar, brown sugar, coconut sugar etc. as batter consistency will be offset.
- Pure vanilla extract: To enhance the flavors.
- Whole wheat flour: See FAQs and recipe notes about possible substitutions.
- Cream cheese and pepitas: Optional for filling but add a few extra layers of flavor.
- Spices: Make your own pumpkin pie spice substitute or purchase one in the spice aisle or your local grocery store.
How to Make Healthy Pumpkin Muffins
- Combine liquid ingredients: In a large bowl, add eggs, a can of pumpkin puree, maple syrup, oil, pumpkin pie spice, baking powder, baking soda and salt. Whisk well until you no longer see white lumps.
- Add flour: Gently stir in the flour. Don’t over mix! Then scoop batter into a prepared muffin tin. I like to use large cookie scoop. Whether to line the muffin cups with parchment paper liners depends how non-stick is your pan.
- Add cream cheese: Amount is completely up to you, I used about 1-2 teaspoons. Make a cavity with a back of a spoon, add 1 teaspoon or more of cream cheese and swirl it with a toothpick.
- Bake for 20 minutes at 375 degrees F: Then cool these little guys in a muffin pan for 5 minutes, then a few more minutes on a wire rack.
Tips for Best Results
- Do not over bake: Bake as per recipe. Even if you insert toothpick into the center of the muffins and it comes out a bit wet, remove muffins from the oven. You don’t want your muffins to turn out dry.
- To replace pumpkin spice blend: Simplify by using 1 teaspoon cinnamon and 1/4 teaspoon each of ginger, nutmeg, cloves and allspice. Alternatively, if your spice drawer is bare, use 2-3 teaspoons of cinnamon.
- Cream cheese products differ: One is softer and you can swirl it, other one is harder and you just bake it as is.
- Don’t use pumpkin pie filling: Make sure not to buy pumpkin pie filling that has added refined sugar and spices. Read the label. Buy a can with “pure pumpkin” label.
How to Store
To store and prevent muffins from drying, place in a resealable bag or airtight container and store on a counter for 3 days. These healthy pumpkin muffins do not contain much oil and rely on pumpkin’s water content to stay fresh.
Freeze baked and cooled muffins in a freezer-safe container same day to ensure freshness. Freeze any muffins for up to 3 months. If you would like them to last longer, wrap each muffin into plastic wrap before placing into a container.
To thaw, just remove muffins from the freezer and let defrost in a bag for a few hours or overnight. Or defrost one in a microwave for a healthy snack.
Storage Tip
For more best muffin storage practices, be sure to check out my posts how to store muffins and how to freeze muffins.
FAQs
You can use the same ratio of whole wheat pastry flour or white whole wheat flour. I have not tested recipe with oat flour, you will need more of it as it’s lighter. All-purpose flour or all purpose gluten free might work but you might need less of it.
For the gluten free version, try my pumpkin muffins with almond flour.
Add up to 1/2 cup of dark chocolate chips, chopped dates, chopped walnuts or any dried fruit like dried cranberries or raisins. A teaspoon of vanilla extract also would be nice!
I suppose you could, it will need to bake longer and you could just swirl the cream cheese at the top. Or you could just make healthy pumpkin bread recipe.
More Healthy Pumpkin Recipes
- Pumpkin chocolate chip bread
- Healthy pumpkin bread
- Almond flour pumpkin bread
- Healthy pumpkin brownies
- Healthy pumpkin bars
- Healthy pumpkin cookies
- Banana pumpkin bread
Healthy Pumpkin Muffins
Equipment
Video
Ingredients
- 2 large eggs
- 1 1/4 cups pumpkin puree, not pumpkin pie filling
- 3/4 cup maple syrup or honey
- 3 tbsp any mild oil, I used avocado oil
- 1 tbsp pumpkin pie spice
- 2 tsp baking powder
- 1 tsp baking soda
- 1/2 tsp salt
- 2 cups whole wheat flour, or spelt flour
- 12 tsp cream cheese, or more
- Pumpkin seeds, for garnish (optional)
Instructions
- Preheat oven to 375 degrees F and spray muffin tin with cooking spray. Set aside.
- In a large mixing bowl, add eggs, pumpkin puree, maple syrup, oil, pumpkin pie spice, baking powder, baking soda and salt; whisk well to combine. Add flour and gently mix until combined.
- Using an ice cream scoop, distribute batter evenly between 12 openings of a muffin tin. Make a cavity with a back of a spoon, add 1 tsp or more of cream cheese, swirl with a toothpick (or leave it) and sprinkle with pumpkin seeds.
- Bake for 20 minutes. Then remove from the oven, let muffins cool for 5 minutes and transfer to a cooling rack to cool off for another 10 minutes. Enjoy!
Notes
- Store: To prevent muffins from drying, place in a resealable bag or airtight container and store on a counter for 3 days.
- Freeze: In an airtight container for up to 3 months.
- Substitute pumpkin spice blend: Use 1 teaspoon cinnamon and 1/4 teaspoon each of ginger, nutmeg, cloves and allspice. Alternately, use 2-3 teaspoon of cinnamon if you are out of all other spices.
- Other flours: You can use the same ratio of whole wheat pastry flour or white whole wheat flour. I have not tested recipe with oat flour, you will need more of it as it’s lighter. All-purpose flour or all purpose gluten free might work but you might need less of it.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Make these for breakfast and they are good i double the recipe and follow the exact step only using one cup of maple syrup and they still came out fantastic.
Fantastic! Glad you reduced the sugar and still enjoyed the recipe!
Hi,
I made the lemon muffins and they were good. My co workers enjoyed them with a cup of coffee. I’m looking to bake the pumpkin muffins, but wondering why the difference in oven temperatures at 375F but the lemon ones were at 350F? Is it because of using puree?
I am not sure which lemon muffins you made so hard to say for me why. 375F would be a temperature for this recipe.
These were wonderful, the only thing is you might want to soften the cream cheese before you try to mix it in otherwise it makes a mess.
Glad it all worked out and you enjoyed it!
I am making this recipe today and want to clarify if the Pure Vanilla Extract you show and mention above the recipe is actually in it, as it is not listed in the actual recipe. If so, how much do you add? Thanks so much! I appreciate recipes that use healthier ingredients vs. processed sugars.
Oh, yes…You can add it or not but overall 1 tsp of vanilla will do wonders to the pumpkin muffins. But without will taste delicious too! Hope this helps.
I made these today, forgot to get cream cheese! I put some pumpkin pie spice and some sugar in a baggie then put muffins in shook bag and coated muffins they came out delicious !
Going to try cream cheese next batch ! This recipe is a keeper!❤️🇺🇲👍
Oh, such a great idea. Like donuts almost. Glad you enjoyed these pumpkin muffins and made your own, Donna. I am sure you will love them with cream cheese too!
Hi, I posted earlier to ask how much vanilla you need? I added a tsp. they turned out great!
So glad to hear it went great!
These are absolutely delicious! I think i may mix the cream cheese with some maple syrup and cinnamon next time! Do you think these would stay fresh longer in the fridge?
So glad you enjoyed them and yum on the cinnamon cream cheese! Yes you could store in the fridge longer if needed, may need to reheat very slightly to warm up again to room temp.