Pumpkin Cream Cheese Muffins are light and fluffy with a rich creamy center, and sweet streusel topping. They’re the perfect breakfast on a cool crisp morning.

If pumpkin is your favorite fall flavor these pumpkin chocolate chip muffins and banana pumpkin muffins are a must try!

Pumpkin cream cheese muffins with streusel topping on parchment paper on a counter.

Simple, delicious, and in season, these pumpkin cream cheese muffins are a win-win-win. Perfectly sweet with layers of flavor, I’m loving this addition to my collection of healthy muffin recipes!

Whether it’s a filling in healthy pumpkin muffins or the topping on a healthy pumpkin cake, cream cheese and pumpkin are a match made in heaven.

Why You’ll Love This Recipe

  • Uses entire can of pumpkin: Just like with healthy pumpkin bread, we use an entire can of pumpkin puree which keeps these pumpkin spice muffins moist for days.
  • Starbucks copycat: You can still hit the drive thru for a PSL, but skip the extra calories with this healthier Starbucks pumpkin cream cheese muffins recipe.
  • Versatile with flour: Make them with white flour for more of a dessert, sort of like a healthy cupcake, or whole wheat flour for a healthy breakfast or snack.
  • Refined sugar free: Naturally sweetened with maple syrup and no added sugar, except the streusel topping.
  • Easy: No electric mixer required! These homemade muffins are easy and make your home smell like a bakery.

Ingredients for Pumpkin Cream Cheese Muffins

Cream cheese pumpkin muffins are made with simple ingredients and warm fall spices, I’m betting you already have most on hand.

Pumpkin puree, all purpose flour, sugar, eggs, maple syrup, pumpkin pie spice, cream cheese, baking powder, baking soda, vanilla, coconut oil, salt.
  • Cream cheese: Bring 5 ounces of plain cream cheese to room temperature, it can be from a block or a tub.
  • Liquid sweetener: If you’re a fan, you know I always sweeten my healthy muffins with maple syrup or honey. For this pumpkin muffin recipe we’ll be using some for the muffin batter, and some for the sweet cream cheese filling.
  • Eggs: 2 large eggs are needed for structure and binding.
  • Pumpkin puree: Pick up the standard 15 ounces canned pumpkin puree, make sure the label does not read pumpkin pie filling. During fall I love making my own pumpkin puree, if you’d like to try it here’s how to cook a pumpkin and make puree out of it.
  • Oil: A mild oil helps make your muffins super moist without adding strong flavor, I recommend avocado oil.
  • Pumpkin pie spice: You can use store-bought or make your own pumpkin pie spice substitute, both add the well loved autumn flavor.
  • Baking essentials: Pure vanilla extract, baking powder, baking soda, and salt.
  • Flour: I used all purpose flour this time for an indulgent treat, but you can also use whole wheat flour.
  • Sugar: A little bit of sugar adds sweetness to the streusel topping. I’m a fan of cane sugar, you can go with any kind of sugar you like.
  • Coconut oil or butter: To bring the streusel together you’ll need room temperature coconut oil or unsalted butter.

How to Make Pumpkin Cheesecake Muffins

Pumpkin cheesecake muffins are divided into three parts: the muffin, the filling, and the crumb topping. Each section is super easy and the total prep time is just 15 minutes.

There’s a full recipe card below.

How to make cream cheese filling and streusel topping for pumpkin muffins.

Preheat your oven to 375 F, spray muffin tin with cooking spray or add muffin liners.

  • Make cream cheese filling: To a medium bowl, whisk the cream cheese and maple syrup together until smooth. Set aside.
  • Make streusel topping: Same simple process as my raspberry muffins. Add flour, sugar, and coconut oil to a small bowl and mash with a fork until small crumbs form.
How to make pumpkin cream cheese muffin batter.
  • Make muffin batter: To a large bowl, add the eggs, pumpkin puree, maple syrup, oil, pumpkin pie spice, vanilla extract, baking powder, baking soda and salt. Whisk well until smooth.
  • Fold in flour: Add flour to the muffin mixture and gently mix just enough to combine.
  • Add first layer of batter: Starting with the first layer, spoon 2-3 tablespoons of muffin batter in each muffin cup.
How to fill pumpkin muffins with cream cheese and top with streusel. Then bake in a muffin tin.
  • Fill muffin pan: Next, add a spoonful of cream cheese filling then equally distribute the remaining pumpkin mixture on top.
  • Top with streusel: Lastly, sprinkle the sweet crumb topping on top.
  • Bake: Bake until a toothpick inserted in the center comes out clean, roughly 22-23 minutes.
  • Cool and enjoy: Remove pumpkin muffins from the oven, let them cool in the pan for the first 10 minutes, then transfer to a wire rack to cool completely.

Tips for Best Results

Make these pumpkin muffins with cream cheese filling the best fall treat with these easy tips.

  • To substitute pumpkin pie spice: Make your own! Mix 1 teaspoon of cinnamon with 1/4 teaspoon each of ginger, nutmeg, cloves, and allspice. Or just use cinnamon, measure with your heart up to 3 teaspoons.
  • Use flour you like: Select from whole wheat flour, spelt flour, white whole wheat flour, or all-purpose flour and sub cup for cup.
  • To hide cream cheese: I like it a bit protruding on top. But for more of a surprise, add only 1 tablespoon of batter to the bottom of muffin tin, then filling, and then majority of batter.
  • Measure flour correctly: This is my top tip to avoid dry muffins. Measure correctly using the scoop and level method, scoop the flour into the measuring cup then level off with the flat edge of a knife.
  • Don’t skip oil: A lot of times people like to substitute with applesauce, but don’t in this case. With its high moisture content you’d have to decrease the puree and both taste and texture will be off.
  • Don’t over bake the muffins: Once your toothpick comes out clean, it’s time to remove them from the oven.
Pumpkin cream cheese muffin sliced in half showing texture and filling inside.


  • Omit streusel: Even without the buttery crisp topping, these pumpkin cream cheese muffins will still be a huge hit.
  • Cinnamon sugar topping: Add a fragrant cinnamon topping like I did with these apple cinnamon muffins, it’s really easy and adds so much flavor! Mix some cinnamon with sugar, brush muffin tops with melted coconut oil or unsalted butter, then dip.
  • Add chocolate chips: Because no one ever turns down a chocolate chip muffin.
  • Sliced almonds: Like in blackberry muffins, a sprinkle of sliced almonds make a wonderful crisp topping.
  • Pumpkin seeds: Add more earthy pumpkin flavor with the addition of pumpkin seeds.
  • Omit cream cheese: You could leave these muffins plain without the creamy filling, or add a dollop of plain Greek yogurt for a tangy pumpkin muffin.
  • Other add-ins: There’s lots of ways to add flavor and texture. Toss in some walnuts, pecans, coconut flakes, raisins, or dried cranberries. If you love cinnamon, you could even swirl some in with the cream cheese filling.

How to Store

Store: Once muffins have cooled, place them in a resealable bag or airtight container. They’ll stay fresh at room temperature for 2-3 days.

Freeze: Store muffins in a freezer safe airtight container and enjoy within 3 months.

Storage Tip

For more best muffin storage practices, be sure to check out my posts how to store muffins and how to freeze muffins.


Can I make these pumpkin muffins with gluten-free flour?

Unfortunately no. Instead, make my almond flour pumpkin muffins and add the filling and crumbly topping.

Can I prepare muffin batter ahead of time?

Yes. Make the pumpkin muffin batter as per recipe but leave out the leveling agents, then cover tightly and refrigerate for up to 24 hours. Add in baking powder and baking soda, make filling and streusel in separate bowls, assemble, and bake as per recipe.

Can I substitute pumpkin puree with anything else?

Swap with pureed butternut squash, acorn squash, or sweet potatoes.

Can I make mini pumpkin cream cheese muffins?

Yes, mini muffins are great for lunch boxes! Follow the same recipe but the total time to bake will decrease to 10-12 minutes. Make sure to test with toothpick.

Can I turn this pumpkin muffin recipe into a loaf?

To make a loaf you’ll need to bake at a lower temperature for longer. Preheat your oven to 350 degrees F and bake for 50-60 minutes until toothpick comes out clean. If you have a mini loaf pan then bake for 25-30 minutes.

More Pumpkin Recipes to Try

Looking down on 12 Starbucks pumpkin cream cheese muffins. Linen towel and parchment paper on a counter.
Pumpkin cream cheese muffin sliced in half showing texture and filling inside.

Pumpkin Cream Cheese Muffins

Pumpkin Cream Cheese Muffins are light and fluffy with rich creamy center, and sweet streusel topping. Perfect breakfast on a cool morning.
4.50 from 2 votes
Servings 12 muffins
Calories 316
Diet Vegetarian
Prep Time 15 minutes
Cook Time 23 minutes
Resting Time 10 minutes
Total Time 48 minutes


For Cream Cheese Filling:

For Streusel Topping:

  • 1/4 cup all-purpose flour or whole wheat flour
  • 2 tablespoons sugar any kind
  • 1 tablespoon coconut oil or butter room temperature

For Muffins:


  • Preheat oven to 375 degrees F and spray muffin tin with cooking spray. Set aside.
  • Make cream cheese filling: In a medium bowl, add cream cheese and maple syrup, then whisk until smooth. Set aside.
  • Make streusel topping: In a small bowl, add flour, sugar and coconut oil. Using a fork, mash until small crumbs form. Set aside.
  • Make muffin batter: In a large mixing bowl, add eggs, pumpkin puree, maple syrup, oil, pumpkin pie spice, vanilla extract, baking powder, baking soda and salt; whisk well to combine. Add flour and gently mix until combined.
  • Spoon 2-3 tablespoons of muffin batter in each opening of a muffin tin, then top with approximately 1 tablespoon of cream cheese filling, and finish with equal amount of remaining batter. Sprinkle streusel topping on top of all muffins.
  • Bake muffins for 22-23 minutes or until toothpick inserted in the center comes out clean. Remove from the oven, let cool for 10 minutes and transfer to a cooling rack to cool off for another 10 minutes. Enjoy!


  • Store: To prevent muffins from drying, place in a resealable bag or airtight container and store on a counter for 2-3 days. Keep lid ajar if muffins start to get soggy.
  • 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.


Serving: 1muffin | Calories: 316kcal | Carbohydrates: 46g | Protein: 6g | Fat: 12g | Saturated Fat: 4g | Trans Fat: 0.003g | Cholesterol: 43mg | Sodium: 312mg | Fiber: 2g | Sugar: 15g
Course: Muffins
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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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!

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  1. 4 stars
    Good breakfast muffin. I need to remember that “healthy” means not as sweet as we are accustomed to. My only problem was the cream cheese didn’t set upon baking. It was still gooey in the middle. Overall, good flavor and texture!

    1. If you want the cream cheese to set, make a small well on top of batter and add it there. It’s not supposed to set when inside the muffin. Enjoy!

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