Pumpkin Cheesecake Muffins

I get it. Baking from scratch may seem like a lot of work. Not only do you have to make sure you have all the ingredients, but you also need to have the time to mix it together. Oh and bake it yet to boot! Hold on, though… Before we go too far down that self-induced too-little-time pity party, you have to admit that when you bite into a warm, fresh from the oven homemade baked good, you are in heaven. In this case, the pumpkin-spice filled clouds burst open and pumpkin cheesecake muffins floated down!

I love that when you bake your own goods at home, you can taste the quality ingredients that make up each bite and you’re cognizant of the time and love that was put into each treat. I know baking doesn’t relax everyone like it does for me, but I also know everyone enjoys something delicious. These pumpkin cheesecake muffins are totally worth the effort, which in all honesty, isn’t really too much. And who doesn’t love anything pumpkin?!

Pumpkin cheesecake muffins sitting in basket fitted with linen towel sitting on wood board

The three layers of this muffin are pure perfection:

  • The pumpkin muffin base is moist and so flavorful.
  • The cheesecake layer has a bit of a soft texture, which is just what you want in this muffin.
  • The streusel topping is that perfect bit of crunch that perfectly caps off the whole experience.

If my (probably over the top) description thus far doesn’t convince you, just picture this. Imagine having the perfect treat to enjoy on a chilly fall morning with a steaming cup of coffee. Yes please!

Pumpkin cheesecake muffins torn in half with cheesecake middle exposed held by hand with extra muffins and cooling rack in background
Doesn’t that cheesecake filling in the middle just look soooo good?! Trust me, it is!

Watch how to make these pumpkin cheesecake muffins:

As always, let me know in the comments if you make these muffins! I’d love to know how much you like/love these!

Pumpkin cheesecake muffins sitting on decorative wire cooling rack on wood board with basket full of muffins and towel in background all on gray slate surface with with background

Pumpkin Cheesecake Muffins

  • Author: Kaleb Wyse
  • Prep Time: 30 minutes
  • Cook Time: 23 minutes
  • Total Time: 53 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert
  • Method: Baking
  • Cuisine: American


Pumpkin is good on its own, but when it’s combined with a cheesecake filling, could it get any better?! Seriously, these pumpkin cheesecake muffins are the best and since they’re topped with a streusel topping, you just can’t go wrong!



For the streusel topping

  • 1/2 cup whole wheat flour
  • 1/2 cup rolled oats
  • 1/2 cup brown sugar
  • 1/4 cup roasted pepitas (pumpkin seeds)
  • 1 teaspoon cinnamon
  • 8 tablespoons butter

For the cheesecake filling

  • 1 8-ounce package cream cheese, room temperature
  • 1/2 cup sugar
  • 1 egg

For the pumpkin muffins

  • 1 cup pumpkin puree
  • 1/2 cup brown sugar
  • 2 eggs
  • 1/3 cup vegetable oil
  • 2 tablespoons molasses
  • 2 teaspoons vanilla extract
  • 1 cup flour
  • 1/2 cup whole wheat flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 1 teaspoon ground ginger
  • 1/2 teaspoon nutmeg
  • 1 teaspoon salt


  1. Preheat oven to 350 degrees.

For the streusel topping

  1. In a medium bowl, combine the whole wheat flour, oats, brown sugar, roasted pepitas and cinnamon. Stir to evenly combine.
  2. Cut butter into small pieces and work into the mixture until it looks like wet sand, as would be done for pastry dough. Set aside.

For the cheesecake filling

  1. In a small bowl, whisk the cream cheese, sugar and egg until smooth with no lumps.

For the muffin batter

  1. Prepare the batter in a large bowl. Whisk the pumpkin puree and brown sugar until smooth.
  2. Whisk in the eggs, oil, molasses and vanilla until combined.
  3. Add the flours, baking powder, baking soda, cinnamon, ginger, nutmeg and salt. Whisk until just combined and no streaks remain.
  4. Line a 12-cup muffin tin with baking liners. Fill each liner 1/3 full with prepared batter. Use an offset spatula to create a well in the center of each muffin.
  5. Evenly portion cheesecake filling into the wells.
  6. Top with remaining muffin batter.
  7. Top with the prepared streusel.
  8. Bake in a preheated oven until puffed and set, 20-23 minutes.
  9. Once baked, remove from oven and cool 15 minutes on a cooling rack.


  • Serving Size: 1 muffin
  • Calories: 418
  • Sugar: 30.2g
  • Sodium: 333.1mg
  • Fat: 22.2g
  • Saturated Fat: 14.1g
  • Trans Fat: 0g
  • Carbohydrates: 50.5g
  • Fiber: 2.8g
  • Protein: 6.2g
  • Cholesterol: 86mg

Keywords: fall, muffins

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