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split in half cream cheese pumpkin muffin in a white bowl

Pumpkin Cream Cheese Muffins

Rich, moist pumpkin muffins are filled with a cheesecake mixture and topped with pumpkin spiced pumpkin seeds. Forget Starbucks Muffins, this is the only pumpkin muffin you will need this fall!   

  • Total Time: 35 minutes
  • Yield: 15 Muffins 1x


Units Scale

Pumpkin Muffin

  • 250 grams (2 Cups) All-Purpose Flour/ Plain Flour
  • 1/2 Teaspoon Baking Powder
  • 1/2 Teaspoon Baking Soda
  • 1 Tablespoon Pumpkin Pie Spice
  • 1/2 Teaspoon salt
  • 200 grams (1 Cup) Dark Brown Sugar
  • 50 grams (1/4 cup) Granulated Sugar
  • 15oz Pumpkin (not pumpkin pie filling)
  • 2 Large Eggs, at room temp.
  • 1 Tablespoon Pure Vanilla Extract
  • 4oz (1/2 Cup) Vegetable Oil

Cheesecake Filling

  • 8oz Cream Cheese, at room temperature
  • 1 Tablespoon Pure Vanilla Extract
  • 1 Large Egg, at room temperature
  • 2 Tablespoon Granulated Sugar

Optional Topping

  • 1 cup Pumpkin Spiced Pumpkin Seeds (Found mine at Trader Joe's)


  1. Preheat oven to 400F/204C and grease a regular sized muffin pan, set aside.
  2. In a large bowl combine the sugars, pumpkin, eggs, vanilla extract and vegetable oil. Mix until fully combined.
  3. In another large bowl mix the flour, baking soda, baking powder, pumpkin pie spice, and salt. 
  4. Slowly fold the dry ingredients into the wet batter, mixing until just a few flour streaks are left.
  5. Scoop the batter evenly into the muffin pan, making sure to fill 3/4 of the way. I prefer to spread the muffins out when baking them, so in a 12 cup muffin pan I would only fill 6 but you can definitley fill each cup if you prefer.
  6. In the bowl of an electric mixer combine the cream cheese, vanilla, and sugar. Once fully combined whisk in the egg and beat until smooth and fully combined, make sure to srap down the sides of the bowl.
  7. Pour the cheesecake batter into a piping bag or into a ziplock bag and snip the corner off. Stick the tip of the piping bag into the center of the muffin and squeeze for a few seconds. Top with pumpkin seeds.
  8. Bake at 400F/204C for 5 minutes then reduce temperature to 350F/180C and bake for an additional 13-15 minutes, or until when you gently touch the center of the muffin it bounces back quickly, or a toothpick inserted in comes out with no wet batter. Let cool on a wire rack for 10 minutes before taking out of the pan. Store in an air-tight container for up to 4 days, I prefer to store them in the fridge after the first day, due to the cream cheese. 


To bake mini muffins start them at the higher tempearture bake for 5 minutes then reduce the temperature and bake for 8-12 minutes or until when touched on the top cernter it bounces back lightly.  

  • Author: Elizabeth Waterson I Confessions of a Baking Queen
  • Prep Time: 10 minutes
  • Cook Time: 25 minutes
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American

Keywords: pumpkin muffin recipe, cheesecake stuffed muffins, cheesecake filled muffins

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