These Pumpkin Cheesecake Muffins give you a soft, spiced pumpkin muffin with a pocket of creamy cheesecake baked right into the center. Plus it's topped off with a buttery cinnamon streusel that gets just a little crisp in the oven. My daughter isn't usually a fan of pumpkin spice anything, and she still devoured these muffins. I was lucky I got any for myself!
Why We Love This Recipe
- Tastes like the coffee shop version, but homemade.
- Two desserts in one. Warm, spiced flavor of a pumpkin muffin and the rich, tangy filling of a cheesecake.
- Wins over the pumpkin spice skeptics. Even in my house, where not everyone reaches for pumpkin spice first, these disappeared fast.
- That streusel topping. It adds a little crunch and a little extra sweetness.
- Simple ingredients. Nothing fancy or hard to find. This is a pantry-and-fridge kind of recipe.
- This recipe makes 18 muffins, so there's plenty for breakfast, an afternoon snack, or a plate to send home with whoever stops by.
Pumpkin Cheesecake Muffin Ingredients
For the pumpkin muffins
- All-Purpose Flour, Baking Soda, and Baking Powder - this combination gives the muffins their structure and a good rise.
- Salt, Pumpkin Pie Spice, and Ground Cinnamon - this is where the warm, cozy fall flavor comes from. Using both pumpkin pie spice and cinnamon gives the muffins a little more depth than pumpkin spice alone. Store-bought pumpkin pie spice works great here, or you can make your own with my homemade pumpkin pie spice recipe.
- Pumpkin Puree - this recipe is written for canned pumpkin puree, which has a consistent, reliable moisture content. I don't recommend swapping in fresh pumpkin puree here, since it can throw off the texture of the batter.
- Granulated Sugar and Brown Sugar - the mix of the two adds sweetness along with a touch of moisture and richness from the brown sugar.
- Canola Oil - or vegetable oil. Keeps these muffins soft and moist for days, rather than drying out like some pumpkin muffins can.
- Eggs and Vanilla Extract - for structure and flavor.
For the cheesecake filling
- Cream Cheese - this is the base of the filling, so let it soften fully at room temperature before you mix it.
- Granulated Sugar, Egg Yolk, Vanilla Extract, Flour - the flour helps the filling set up instead of staying too loose once baked.
For the streusel topping
- Flour, Brown Sugar, Cinnamon, and Salt - a simple streusel base.
- Melted Butter - brings it all together into that crumbly, slightly crisp topping.
How To Make Pumpkin Cheesecake Muffins
Start by preheating your oven to 350°F and lining two muffin pans with paper liners. You'll need 18 total.
In one bowl, whisk your dry ingredients together: flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon. Set that aside.
In a second bowl, stir together the pumpkin puree, both sugars, oil, eggs, and vanilla until the mixture is smooth and well blended.
Add the dry ingredients into the wet ingredients, stirring gently just until you no longer see streaks of flour.
This is the step to be careful with, mix only until combined for tender muffins.
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For the filling, beat the softened cream cheese with the sugar, egg yolk, vanilla, and flour until it's smooth and creamy with no lumps.
To assemble, use a regular-size ice cream scoop to portion the pumpkin batter into your liners until each one is about half full. Add a spoonful of the cheesecake filling to the center of each muffin, right on top of the batter, and press it down gently so it doesn't sit too high above the batter.
Stir together your streusel ingredients.
Sprinkle a bit over the top of every muffin before they go in the oven.
Bake for 20 to 22 minutes. You'll know they're ready when the tops are set and a toothpick inserted into the pumpkin portion (avoiding the cheesecake center) comes out clean.
More Pumpkin Recipes to Try
If you're in a pumpkin kind of mood, I have a few more recipes worth adding to your list. My Pumpkin Pancakes made with pancake mix are a quick way to bring pumpkin spice to your breakfast table using a shortcut you probably already have in your pantry. For something sweet, my Pumpkin Snickerdoodles combine the classic cinnamon-sugar cookie with cozy pumpkin flavor. And if you want a dessert for a crowd, my Pumpkin Bundt Cake with Orange Glaze is a moist, spiced cake finished with a bright citrus glaze that balances the warm spices perfectly.
Making Mini Pumpkin Muffins
I like to make 12 full-size muffins and 12 mini muffins, baking them both at the same time. For the mini muffins, I used a cookie scoop for the batter and teaspoon for the cheesecake filling, so the portions stayed just right for the smaller size.
The mini muffins only need 10 to 15 minutes in the oven and came out perfectly, so keep a close eye on them and pull them well before your full-size batch is done.
Pumpkin Cheesecake Muffin FAQs
I don't recommend it for this recipe. This recipe is written and tested with canned pumpkin puree, and fresh pumpkin puree can add extra moisture that changes the texture of the batter.
Yes! Mini muffins bake up beautifully with this batter. Fill your mini muffin tin the same way you would the full-size version, and start checking for doneness at 10 minutes. They'll likely be done between 10 and 15 minutes.
Yes. Let them cool completely, then wrap them individually with plastic wrap before transferring to a freezer-safe bag or container. They'll keep well for up to 2 months. Thaw in the refrigerator overnight and bring to room temperature before serving.
Cold cream cheese is the most common culprit. Let it sit out until it's fully softened to room temperature before mixing, and it will blend into a smooth, creamy filling.
Mom Tip
Don't you just hate it when the muffin sticks to the paper liner? Letting the muffins properly cool will help with this issue. If I am really in a hurry to try muffins that are still warm, I'll pop one (or two) in the fridge for a few minutes to hurry up the cooling process. Or, you could always coat the pan well with nonstick cooking spray first and skip the liners.
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Complete Recipe
Pumpkin Cheesecake Muffins
Ingredients
For the pumpkin muffins:
- 1 ¾ cups All-Purpose Flour
- 1 teaspoon Baking Soda
- 1 teaspoon Baking Powder
- ½ teaspoon Salt
- 2 teaspoons Pumpkin Pie Spice
- 1 teaspoon Ground Cinnamon
- 1 cup Pumpkin Puree canned
- ¾ cup Granulated Sugar
- ½ cup Brown Sugar
- ½ cup Canola Oil or vegetable
- 2 large Eggs
- 1 teaspoon Vanilla Extract
For the cheesecake filling:
- 8 ounces Cream Cheese softened
- ⅓ cup Granulated Sugar
- 1 large Egg Yolk
- 1 teaspoon Vanilla Extract
- 2 tablespoons All-Purpose Flour
For the streusel:
- ¼ cup All-Purpose Flour
- 2 tablespoons Brown Sugar
- ½ teaspoon Ground Cinnamon
- Pinch Salt
- 2 tablespoons Butter melted
Instructions
- Preheat the oven to 350°F. Line two 12-cup muffin pan with 18 paper liners.
- In a medium bowl, whisk together the flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon.
- In a larger bowl, mix the pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla extract until smooth.
- Gradually add the dry ingredients to the pumpkin mixture, stirring just until combined. Do not overmix.
- In a small bowl, beat the cream cheese, sugar, egg yolk, vanilla extract, and flour until smooth and creamy.
- Fill each muffin cup about halfway with pumpkin batter. Add a spoonful of the cheesecake mixture to the center of each muffin.
- Mix the ingredients for the streusel together. Sprinkle the streusel mixture on top of each muffin.
- Bake the muffins for 20 to 22 minutes, or until the muffins are set and a toothpick inserted into the pumpkin portion comes out clean.
Notes
- Don't overmix the batter once you add the dry ingredients - mix just until the flour disappears to avoid gummy muffins.
- Soften the cream cheese fully before making the filling, or it will turn out lumpy.
- Use canned pumpkin puree, not fresh since fresh puree adds too much moisture.
- Let muffins cool completely on a wire rack before removing liners to prevent sticking.
- Mini muffin option: I like to make 12 mini muffins and 12 regular size muffins with this recipe. Bake mini muffins 10-15 minutes; check at the 10-minute mark.
- Use an ice cream scoop for muffin batter and a cookie scoop for mini muffins and the cheesecake filling.
- Press the filling down slightly so it doesn't sit too high above the batter.
- Store in the fridge up to 5 days. Let cold muffins come to room temperature for the creamiest texture.
- Freezes well for up to 2 months. Cool first, wrap individually, then transfer to a freezer bag.
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