Healthy Pumpkin Muffins are light and moist, made with whole wheat flour, a dollop of cream cheese and chock full of mouth-watering fall spices. They are perfect for breakfast!

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.

Don’t let pumpkin season pass you by! Other seasonal recipes that help make this transition include healthy pumpkin soup and pumpkin chia pudding!

Baking recipes with pumpkin spice flavor fill my kitchen with warm delicious smells of autumn.

These 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!

That makes them perfect for healthy snacks.

I am beginning to have quite a knack for transforming favorite restaurant (or coffee shop) recipes into their healthier, budget-friendly versions like sous vide egg bites!

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

Why We Love This Recipe

  • Whole grains, healthy fats and no refined sugar: Healthified version of your favorite Starbucks pumpkin cream cheese muffin!
  • Wholesome ingredients: Including pure pumpkin puree which is an amazing source of fiber.
  • Easy to make: Basic ingredients and in one bowl – 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 warming 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.
  • Canned pumpkin puree: You can use homemade puree as well, although it is often a bit more watery. It should be OK.
  • Eggs: To add lift and binding in baked goods. 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 seasonal touch that maple syrup adds, but honey can be used as well. Please do not use sugar as batter consistency will be offset.
  • Pure vanilla extract: Used to enhance the flavors, use pure not imitation.
  • Whole wheat flour or spelt flour: I used spelt flour but whole wheat flour works just as good!
  • 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 puree is the same as canned pumpkin. Homemade pumpkin puree works as well.

Make sure not to buy pumpkin pie filling that has added 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. This step eliminates old fashioned way of mixing wet and dry ingredients separately.

Then add 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 pan. I like to use an ice cream scoop!

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 teaspoon. 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 and it comes out a bit wet, remove muffins from the oven.

You don’t want to over bake this pumpkin muffin recipe. Cool on 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. You want to keep muffins sealed.

Freeze baked and cooled muffins same day to ensure freshness. Freeze any healthy muffins for up to 3 months.

To thaw just remove muffins from the freezer and let defrost in a bag for a few hours or overnight.

Enjoy these copycat healthified ‘Starbucks’ low fat pumpkin muffins at home without the guilt or a hefty bill.

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 almond flour pumpkin muffins.

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.

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

Healthy Pumpkin Muffins are light and moist, made with whole wheat flour, a dollop of cream cheese and chock full of cozy fall spices.
5 from 16 votes
Servings 12 muffins
Calories 201
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!

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Comments

  1. 5 stars
    New favorite pumpkin muffins! I’ve been baking the same recipe for years, and it is tasty… but full of processed sugar. I made this with all white wheat flour and maple syrup. So good!

  2. If you don’t have aluminum free baking powder can you still use it in the Health Pumpkin Muffins (Starbucks Copycat)?

  3. Hi, I’m planning on making pumpkin muffins and love several of yours recipes. What is the difference (flavor, texture) in your “Pumpkin chocolate chip bread”(can be made as muffins) and these “Pumpkin muffins”?

  4. Happy fall!!! I’m so excited to try theSe healthy pumpkin muffins! Do you happen to have the weight (in grams) of flour used? I’ll be using fresh milled flour and the measurements are usually quite off. I googled a conversion but was just curious if you have it handy. Thanks!!

  5. 5 stars
    Hi Olena,

    I made the pumpkin muffins, Delicious!!!! The only thing I omitted was the cream cheese, since I didn’t have it on hand but added a handful of crushed mixed nuts. Great recipe. Thank you.

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