Pumpkin Cream Cheese Muffins

This post may contain affiliate links. Please read our disclosure policy.

Just like a tasty pumpkin roll, these pumpkin cream cheese muffins blend well-spiced pumpkin muffins with creamy cream cheese filling. Add a crumbly brown sugar topping, and you get delicious pumpkin spice Fall breakfast!

A pumpkin cheesecake muffin with a bite missing

The Best Pumpkin Cheesecake Muffins

These pumpkin cheesecake muffins are fantastic because they taste like having dessert for breakfast. The pumpkin spice flavor is so deliciously tempting and the cream cheese filling adds just the right touch of sweetness. They do have similar elements to pumpkin roll, just without the work.

Whether you are traveling for the holidays or just heading to visit a friend, you can easily take them with you and share the goodness. Plus, they stay wonderfully moist and soft for days, offering a combination of pumpkin coffee cake and pumpkin swirl cheesecake all in one.

Looking for more pumpkin muffin recipes? Try banana pumpkin muffins or pumpkin muffins with streusel topping.

Pumpkin cream cheese muffins stacked on top of each other

Why You’ll Love These Pumpkin Cream Cheese Muffins

You won’t regret making these pumpkin cheesecake muffins. Here’s a few reasons they’re one of our favorites.

  • All the flavors of pumpkin roll. With the rich pumpkin muffin and the creamy filling, these muffins are very reminiscent of a classic pumpkin roll cake, without the work.
  • Perfectly spiced. These muffins use pumpkin pie spice plus a few individual spices, which helps the pumpkin flavor stand out against the cream cheese filling.
  • Creamy cheesecake filling. These pumpkin cream cheese muffins feature a cheesecake-like filling made from cream cheese and powdered sugar. It’s rich, creamy, and a wonderful contrast to the muffins.
A pumpkin cream cheese muffin cut in half

What You’ll Need

These pumpkin cream cheese muffins are made with classic muffin ingredients plus pumpkin puree, spices, and cream cheese.

  • Cream cheese – For the cream cheese filling. Be sure it’s softened to room temperature first.
  • Confectioners sugar – Sweetens the cream cheese filling.
  • Eggs – Give the muffin structure to hold the cream cheese filling.
  • Sugar – White sugar sweetens the muffin.
  • Pumpkin puree – You can grab a can of Libby’s at the store or use my homemade pumpkin puree.
  • Canola oil – Helps keep the muffins extra moist.
  • Flour
  • Spices – Ground cinnamon, nutmeg, cloves, and pumpkin pie spice blend give these pumpkin muffins a lovely warm flavor.
  • Salt – Helps to balance out the sweet ingredients.
  • Butter – Chilled salted butter helps hold the topping ingredients together.
Pumpkin cream cheese muffins in a muffin pan

How to Make Pumpkin Cream Cheese Muffins

Though these pumpkin cheesecake muffins may look fancy, they’re quite simple and straightforward to make.

  • Make the Cream Cheese Filling: Using a stand mixer beat the cream cheese and powdered sugar together until light and fluffy.
  • Prepare the Muffin Batter: Beat the wet ingredients together in the bowl of the stand mixer. In a separate bowl, combine the dry ingredients. Slowly add the dry ingredients to the wet ingredients until just combined. Cover the batter and chill for 20 minutes.
  • Make the Topping: Add the ingredients to the bowl and combine using a pasty cutter or two butter knives to cut the butter into the dry ingredients. The mixture will resemble coarse crumbles.
  • Make the Muffins: Spoon a tablespoon of the chilled batter into the muffin pan. Slice the chilled filling into 24 equal parts and place a piece in each muffin cup. Fill the rest of the paper liners almost to the top with muffin batter. Add a tablespoon of topping to each muffin. Bake and then remove and then cool completely.
A pumpkin cheesecake muffin with a bite misisJust like a tasty pumpkin roll, these pumpkin cream cheese muffins blend well-spiced pumpkin muffins with creamy cream cheese filling.ng

Tips & Variations

These are so many different ways to make these pumpkin cream cheese muffins your own. Here are a few ideas.

  • Add a mix-in Add chocolate chips to the pumpkin muffin batter for a delightful chocolate-pumpkin fusion or mix in chopped nuts, like pecans or walnuts for added crunch and flavor.
  • Make them sweeter. Drizzle maple syrup on top for a hint of sweetness that pairs perfectly with pumpkin.
  • Add dried fruit. Incorporate dried cranberries or raisins to give a fruity twist to the muffins.
  • Layer the cinnamon sugar. Create a cinnamon swirl by layering cinnamon-sugar mixture between the muffin batter and cream cheese filling.
  • Use a mini muffin pan. Make mini versions for bite-sized treats that are perfect for sharing.
  • Make them gluten free. Use gluten-free flour to cater to those with dietary restrictions.
Overhead view of a pumpkin cheesecake muffin

Proper Storage

These pumpkin cheesecake muffins store very well! Here’s how.

  • Fridge. Store pumpkin cream cheese muffins in an airtight container or covered with plastic in the fridge. They will last for up to 4 days.
  • Freezer. Once the pumpkin cream cheese muffins have cooled completely, place them in a freezer bag and store them for up to 3 months. To thaw them out, set them out so they can get to room temperature before eating. If you’re in a hurry, you can heat them up individually for 30 seconds.

More Easy Muffin Recipes

5 from 10 votes

Pumpkin Cream Cheese Muffins

Just like a tasty pumpkin roll, these pumpkin cream cheese muffins blend well-spiced pumpkin muffins with creamy cream cheese filling. Add a crumbly brown sugar topping, and you get delicious pumpkin spice Fall breakfast!
Servings: 24 muffins
Prep: 20 minutes
Cook: 21 minutes
Chill Time: 2 hours
Total: 2 hours 41 minutes


For the cream cheese filling:

  • 8 ounces cream cheese , softened to room temperature
  • 1 cup confectioners sugar sifted

For the batter:

  • 4 large eggs beaten
  • 2 cups white sugar
  • 15 ounce pumpkin puree
  • 1 1/4 cups canola oil
  • 3 cups all-purpose flour
  • 1 teaspoon ground cinnamon
  • 1 teaspoon ground nutmeg
  • 1/2 teaspoon ground cloves
  • 1 1/2 tablespoons pumpkin pie spice blend
  • 1 teaspoon kosher salt
  • 1 1/2 teaspoons baking soda

For the topping:


  • In the bowl of a stand mixer, combine cream cheese and confectioners sugar and beat for 3-4 minutes, until light and fluffy.
  • Scoop filling onto a large rectangle of cling wrap in a 1 1/2 inch wide log shape. Wrap filling tightly with cling wrap and twist the ends of the cling wrap to seal.
  • Place in the freezer and chill for at least 2 hours.
  • Place muffin liners in two muffin tins and set aside.
  • In the bowl of a stand mixer, beat together eggs, sugar, pumpkin puree, and canola oil until well combined. In a medium bowl, whisk together flour, cinnamon, nutmeg, cloves, pumpkin pie spice blend, salt, and baking soda.
  • Add dry mixture to the bowl of the stand mixer and mix until just combined.
  • Cover bowl with cling wrap and chill in the refrigerator for 20 minutes.
  • Preheat oven to 425F.
  • To prepare the topping, combine sugar, flour, and cinnamon in a medium bowl and whisk.
  • Add chilled butter and use a pastry cutter or two butter knives to cut the butter into the mixture until mixture resembles coarse crumbs.
  • Spoon about a tablespoon of batter into each muffin liner.
  • Slice the chilled filling into 24 equal pieces and place into each muffin cup. Evenly disperse the rest of the batter between the muffin cups, filling each muffin liner almost to the top.
  • Spoon a tablespoon of the topping on top of each muffin cup and bake for 6 minutes.
  • Reduce oven temperature to 350F and bake for an additional 15 minutes.
  • Let cool in the pan for 5 minutes before transferring muffins to a wire cooling rack to cool almost completely.

Last Step:

Please leave a rating and comment letting us know how you liked this recipe! This helps our business to thrive and continue providing free, high-quality recipes for you.



Calories: 325kcal | Carbohydrates: 43g | Protein: 4g | Fat: 16g | Saturated Fat: 3g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 8g | Trans Fat: 0.2g | Cholesterol: 36mg | Sodium: 266mg | Potassium: 97mg | Fiber: 1g | Sugar: 28g | Vitamin A: 2891IU | Vitamin C: 1mg | Calcium: 51mg | Iron: 1mg