Pumpkin Muffins with Cheesecake Filling

Last Updated on November 24, 2022 by Jacqueline Rafidi

These are honestly the best pumpkin muffins with cheesecake filling ever.

There has to be that one signature pumpkin dessert you make every year during the fall, right? Well let THIS be that one! These pumpkin muffins with cheesecake filling are fluffy and filled with spice flavor and we are not skimping on the cheesecake filling. They’re also topped with a crispy, streusel crust and best of all – they can be frozen! I recommend removing the paper liners before freezing. When you’re ready to reheat, stick it in the microwave for 30-45 seconds and BOOM. You have fall in the palm of your hands.

How to make these pumpkin muffins with cheesecake filling

When you make these pumpkin cheesecake muffins, comment down below and rate this recipe to let me know your thoughts! Also share a picture or tag me on Instagram @thebitewithjackie, I love seeing your remakes!

The BEST Pumpkin Cheesecake Muffins

The absolute best pumpkin cheesecake muffin
5 from 1 vote
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Course Breakfast, Dessert
Cuisine American
Servings 14 muffins


For the muffin:

  • 1/3 cup vegetable oil
  • 2 eggs
  • 1 cup pumpkin puree NOT pumpkin pie filling
  • ¼ cup milk
  • 1 teaspoon vanilla extract
  • ½ cup brown sugar
  • 1/3 cup granulated sugar
  • 1 ½ cup all purpose flour
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt
  • 1 tablespoon pumpkin pie spice
  • 1 teaspoon ground cinnamon

For the filling:

  • 8 oz cream cheese softened at room temp
  • 1 teaspoon vanilla
  • ¼ cup powdered sugar

For the Streusel Topping:

  • cup brown sugar
  • 3 Tablespoons all purpose flour
  • 1 teaspoon pumpkin pie spice
  • ¼ cup unsalted butter cold and cubed


  • Preheat your oven to 375F.
  • In a large mixing bowl, combine the vegetable oil, eggs, pumpkin puree, milk, vanilla extract and both sugars. Mix until well combined and smooth. Stir together the flour, baking powder, baking soda, salt, pumpkin pie spice and cinnamon and add them into the wet ingredients. Mix just until combined and no lumps appear.
  • Work on your filling mixture by combining all filling ingredients until smooth
  • Make the streusel topping by combining all ingredients together and smashing with a fork until the cold butter is about the size of peas.
  • Prepare 2 cupcake tins (this batter makes 14 cupcakes, or you can make larger cupcakes in just one cupcake tin) and place liners in each mold. Take a small cookie scoop and place one scoop of batter into each liner. Place a heaping tablespoon of the cheesecake filling into each mold on top of the batter. Take another small scoop of the batter and cover each scoop of cheesecake filling. Top each muffin with about a tablespoon of streusel (or as much/little as you like). Bake these for 20 minutes or until fully cooked through. Let them cool slightly before serving – the cheesecake filling will be VERY hot coming straight out of the oven. Enjoy!
Keyword Cheesecake, Pumpkin, Pumpkin Cheesecake Muffins, The BEST Pumpkin Cheesecake Muffins

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  1. These were a hit on thanksgiving, and so quick to make! They have the right amount of pumpkin flavor and the cream cheese in the middle just took them over the top

  2. 5 stars
    This was the best muffin I’ve ever had in my life! Followed the recipe as written. May seem like there’s a lot of steps but it’s easy process and it’s sooo worth it. This is a great recipe!!!

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