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, healthy apple muffins and healthy carrot muffins are among our favorite recipes to make.

Healthy Pumpkin muffins with cream cheese and pumpkin seeds on top.

Healthy pumpkin muffins recipe 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!

And such an easy muffin recipe, they will quickly become your new favorite!

I love to transform favorite restaurant recipes into their healthier, budget-friendly versions like sous vide egg bites. And there are many reasons to love to do so!

Showing texture of inside of pumpkin muffin on a cooling rack.

Why We Love This Pumpkin Recipe

  • Low sugar and low fat: Starbucks pumpkin cream cheese muffin contains 14 grams of fat and 34 grams of sugar. These delicious 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 later to enjoy while viewing fall colors or after visiting the pumpkin patch!
  • Craving satisfied: Move over PSL, these are the best healthy pumpkin muffins with warm spices that hit the spot!

Ingredients and Notes

Whole wheat flour, pumpkin puree, maple syrup, cream cheese, eggs, pumpkin pie spice, baking powder, baking soda, vanilla extract.

For the best pumpkin muffins results, you will need following ingredients:

  • Canned pumpkin puree: You can use homemade pumpkin puree as well, although it is often a bit more watery. It should be OK. Here is a quick tutorial how to roast pumpkin and make pumpkin puree.
  • Eggs: No need for room temperature, we are keeping pumpkin spice muffins easy. 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: I like the pumpkin season touch that natural sweeteners like pure maple syrup and honey add. Please do not use any sugar like white sugar, brown sugar, coconut sugar etc. as batter consistency will be offset.
  • Pure vanilla extract: Used to enhance the flavors, use pure not imitation.
  • Whole wheat flour: See FAQs and recipe notes about possible substitutions.
  • Cream cheese and pepitas: Optional for filling, but if you are craving Starbucks pumpkin cream cheese muffin, this will satisfy.
  • Spices: Make your own pumpkin pie spice substitute blend or purchase at your grocer in the spice aisle.

Recipe Tip

All out of pumpkin spice blend? Simplify by using 1 teaspoon cinnamon and 1/4 teaspoon each of ginger, nutmeg, cloves and allspice. Alternately, if your spice drawer is bare, use 2-3 teaspoon of cinnamon (depending on your love of cinnamon!) and call it good.

Is Pumpkin Puree the Same as Canned Pumpkin?

Yes. Pumpkin purée is the same as canned pumpkin. DIY pumpkin puree works as as well in baked goods and pretty much all pumpkin recipes.

Make sure not to buy pumpkin pie filling that has added refined sugar and spices. Read the label.

How to Make Healthy Pumpkin Cream Cheese Muffins

This healthy pumpkin muffin recipe is easy like any of my healthy muffins. One bowl because life, am I right?!

Whisked eggs, pumpkin puree, maple syrup and spices in a bowl with whisk.

First whisk the eggs in large bowl. This step eliminates old fashioned way of mixing wet ingredients and dry ingredients separately.

Then add 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.

Honey Tip

If using honey, it takes a bit more effort to combine with other ingredients. Make sure honey is liquid or warm up solid honey on the stove or in a microwave. Add flour and gently stir with spatula. I let flour sit and absorb liquids for a few seconds before stirring again.

Pumpkin muffin batter in a bowl with spatula.

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.

Now you are ready to bake your muffins or add optional but or so good cream cheese filling.

Using toothpick to swirl cream cheese into muffins.

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 tsp or more of cream cheese and swirl it with a toothpick.

Cream Cheese Tip

Cream cheese products differ. One is softer and you can swirl it, other one is harder and you just bake it as is.

Bake for 20 minutes at 375 degrees F. 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 to over bake this pumpkin muffin recipe. Cool these little guys in a muffin pan for 5 minutes, then a few more minutes on a wire rack.

Four healthy pumpkin muffins with cream cheese and pepitas on a plate.

How to Store These Muffins

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. The best muffins are sealed in an airtight container muffins!

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.

FAQs

What other flour can I use?

You can use the same ratio of whole wheat pastry flour or white whole wheat flour. I have not tested recipe with oat flour but you could try. I think muffins will be more dense. 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.

What else can I add?

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!

Can I make this into pumpkin bread instead of muffins?

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.

Enjoy these copycat ‘Starbucks’ pumpkin muffins made healthy at home without the guilt with a cup of coffee. Not only are these low fat pumpkin muffins, they are also low calorie and low sugar compared to any other recipe out there!

And of course, no coffee shop can beat homemade pumpkin muffins.

More Healthy Pumpkin Recipes

Other Healthy Muffin Recipes

Close up of healthy pumpkin cream cheese muffin on baking rack.
healthy pumpkin muffins

Healthy Pumpkin Muffins

These Healthy Pumpkin Muffins are low sugar, low fat and yet sweet and moist fall breakfast, healthy snack or dessert.
5 from 26 votes
Servings 12 muffins
Calories 201
Diet Low Fat
Diet Low Fat
Prep Time 10 minutes
Cook Time 20 minutes
Resting Time 10 minutes
Total Time 40 minutes

Ingredients 
 

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!

Video

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 but you could try. I think muffins will be more dense. All-purpose flour or all purpose gluten free might work but you might need less of it. For the gluten free version, try my almond flour pumpkin muffins.

Nutrition

Serving: 1muffin | Calories: 201kcal | Carbohydrates: 35g | Protein: 4g | Fat: 7g | Saturated Fat: 2g | Cholesterol: 33mg | Sodium: 312mg | Fiber: 3g | Sugar: 19g
Course: Muffins
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

5 Secrets to Easy Healthy Dinners

Plus sign up for weekly emails with recipes to make your cooking stress free, delicious and healthy.

About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

Pin this recipe now to save it for later

Pin Recipe

You may also like

Comments

  1. 5 stars
    This recipe sounds great! Can I use reduced fat cream cheese? Do you think it will make a big difference?

  2. 5 stars
    This recipe has become a standby. I use our favorite squash that we grow in our garden, North Georgia Roaster. I made these muffins to give to neighbors at Christmas. One neighbor remarked that it was the best muffin she had ever eaten! Since then we practically always have a batch in the kitchen for breakfast or for a healthy snack. The addition of the cream cheese in the muffin is genius. Thank you so for this recipe. I will be making it always!

  3. 5 stars
    Been waiting for it to cool down outside before I starting baking with pumpkin again. Today was the day. This was a perfect start to the season!

  4. 5 stars
    These were delicious. Really moist and easy to make.They had a hint of sweetness without being too sweet. I ended up using half honey and half maple syrup and whole wheat flour and they turned out great. I made half with chocolate chips for the kids and half with cream cheese for myself. The kids ended up wanting to eat the cream cheese ones and loved them! I was sad that I ran out of pumpkin so I could make 2 more batches! Great job Olena!

  5. 5 stars
    Olena, these were so delicious. The only thing I did differently was use toasted walnuts rather than the Pumpkin seeds. I have been baking for awhile now to eat healthier and had no idea until this recipe that you don’t have to use any oil or butter in the batter. Thanks again for another great recipe I will make again shortly.

    1. 🙂 Yes you don’t because pumpkin puree is enough to make muffins moist. Applesauce and Greek yogurt act the same way.:) Enjoy!

Leave a Reply

Your email address will not be published.

Recipe Rating




This site uses Akismet to reduce spam. Learn how your comment data is processed.