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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 them 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 as 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?!

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!

Watch how to make these pumpkin cheesecake muffins:
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Pumpkin Cheesecake Muffins

Ingredients
For the streusel topping
- ⅓ cup whole wheat flour
- ⅓ cup rolled oats
- ⅓ cup light brown sugar
- ⅓ cup roasted pepitas (pumpkin seeds) or nut of choice, chopped
- 1 tsp ground cinnamon
- 5 tbsp unsalted butter
For the cheesecake filling
- 6 oz cream cheese room temperature
- ⅓ cup granulated sugar
- 1 large egg
For the pumpkin muffins
- 1 cup pumpkin puree
- ½ cup light brown sugar
- ⅓ cup vegetable oil
- 2 large eggs
- 2 tbsp molasses
- 1 tsp vanilla extract
- 1 cup all-purpose flour
- ½ cup whole wheat flour
- 1 tsp baking powder
- ½ tsp baking soda
- 1 tsp ground cinnamon
- 1 tsp ground ginger
- ¼ tsp ground nutmeg
- 1 tsp kosher salt
Instructions
- Preheat oven to 350°F.
For the streusel topping
- In a medium bowl, combine the whole wheat flour, oats, brown sugar, roasted pepitas, and cinnamon. Stir to evenly combine.⅓ cup whole wheat flour, ⅓ cup rolled oats, ⅓ cup light brown sugar, ⅓ cup roasted pepitas (pumpkin seeds) or nut of choice, chopped, 1 tsp ground cinnamon
- 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.5 tbsp unsalted butter
For the cheesecake filling
- In a small bowl, whisk the cream cheese, granulated sugar, and egg until smooth with no lumps.6 oz cream cheese, ⅓ cup granulated sugar, 1 large egg
For the muffin batter
- Prepare the batter in a large bowl. Whisk the pumpkin puree and brown sugar until smooth.1 cup pumpkin puree, ½ cup light brown sugar
- Whisk in the eggs, oil, molasses, and vanilla extract until combined.⅓ cup vegetable oil, 2 large eggs, 2 tbsp molasses, 1 tsp vanilla extract
- Add the all-purpose flour, whole wheat flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Whisk until just combined and no streaks of flour remain.1 cup all-purpose flour, ½ cup whole wheat flour, 1 tsp baking powder, ½ tsp baking soda, 1 tsp ground cinnamon, 1 tsp ground ginger, ¼ tsp ground nutmeg, 1 tsp kosher salt
- Spray a 12-cup muffin tin with nonstick baking spray. Pour the prepared cheesecake batter into the muffin batter. Fold together sparingly until the mixture looks just swirled. Using a half-cup ice cream scoop, divide batter among the prepared muffin tins.
- Top with the prepared streusel.
- Bake in a preheated oven until puffed and set, 20-23 minutes.
- Once baked, remove from oven and cool 15 minutes on a cooling rack.
Video

Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.

Did you make this? Leave a comment below!
love your recipes! you remind of when i grew up cooking and baking with my great aunt. good memories cooking with family.
Just made these muffins now. Smell delicious. There is a lot of batter so muffins are filled to the brim. There is quite a bit more streusel topping than is needed.
I find it takes at least 33 minutes to bake like someone else has mentioned. Can hardly wait to taste them.
I am from Port Hood, Cape Breton in Canada and have just made your pumpkin cheesecake muffins. They are delicious. My new favorite muffin. Thank you for sharing your recipes. I will definitely make these again.
I made this outstanding recipe today. Our family loved them! Thanks for sharing it.
I bake for a little assisted living memory care home and will definitely make these in the very near future. I can tell this is going to be a five-star wonder.
I just have to ask wherever did you find such a cute cooling rack?