These pumpkin cheesecake muffins are a perfect treat for fall! With a warm and spicy pumpkin flavor, they have a creamy cheese filling that makes every bite delightful.
I can’t resist these muffins, especially when they come out warm from the oven. Pair them with a cup of coffee, and you have a cozy snack! 🍂
Key Ingredients & Substitutions
Pumpkin Puree: Fresh pumpkin is great, but canned pumpkin puree is so convenient. Just make sure it’s pure pumpkin, not pumpkin pie filling which has added sugar and spices!
Cream Cheese: If you’re looking for a lighter option, consider using Neufchâtel cheese. It’s lower in fat and works just as well! For a dairy-free version, look for vegan cream cheese.
Spices: You can mix up the warm spices! If you love cinnamon, increase its amount, or sprinkle in some allspice. No nutmeg on hand? You can leave it out or use more cinnamon instead.
Sour Cream: Swap the sour cream with Greek yogurt for a similar tang and extra protein. It also keeps the muffins super moist!
How Do I Get the Muffins to Rise Perfectly?
Getting that perfect rise is key for fluffy muffins! Make sure your baking powder and baking soda are fresh; old leavening agents won’t do the job.
- Don’t overmix the batter! Mix until just combined to keep the muffins light and airy.
- Fill muffin cups only ¾ full. This gives enough room for the muffins to rise without overflowing.
- Preheat your oven! A hot oven helps the muffins lift right from the start, creating a nice dome shape.

How to Make Pumpkin Cheesecake Muffins With Cream Cheese Filling
Ingredients You’ll Need:
For the Muffin Batter:
- 1 ¾ cups all-purpose flour
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- 1 teaspoon ground cinnamon
- ½ teaspoon ground nutmeg
- ½ teaspoon ground ginger
- ¼ teaspoon ground cloves
- ¼ teaspoon salt
- ½ cup unsalted butter, softened
- 1 cup granulated sugar
- 2 large eggs
- 1 15-ounce can pumpkin puree (about 1 ¾ cups)
- ½ cup sour cream or plain yogurt
- 1 teaspoon vanilla extract
For the Cream Cheese Filling:
- 8 ounces cream cheese, softened
- ¼ cup granulated sugar
- 1 large egg
- 1 teaspoon vanilla extract
How Much Time Will You Need?
This recipe takes about 15 minutes to prepare and around 22-26 minutes to bake. You’ll want to give them 10 minutes to cool in the pan afterward, making your total time about 45 minutes from start to enjoying these delicious muffins!
Step-by-Step Instructions:
1. Preheat the Oven:
First, I’m going to get my oven all warmed up. Preheat it to 350°F (175°C) and line a 12-cup muffin pan with paper liners or grease it well to prevent sticking.
2. Mix the Dry Ingredients:
In a medium-sized bowl, I’ll whisk together the flour, baking powder, baking soda, and all the warm spices—cinnamon, nutmeg, ginger, cloves, and salt—until everything is mixed well. This will make sure my batter is nicely flavored!
3. Cream the Butter and Sugar:
In a larger bowl, I’m going to beat the softened butter and sugar together using a hand or stand mixer until it’s creamy and smooth. It should look fluffy and delicious!
4. Add the Eggs and Wet Ingredients:
Next, I’ll add the eggs one at a time, mixing well after each addition to ensure they’re fully incorporated. After that, I’ll mix in the pumpkin puree, sour cream (or yogurt), and vanilla extract until it’s all nice and smooth.
5. Combine Dry and Wet Ingredients:
Now it’s time to carefully add my dry ingredients to the wet ones. I’ll mix just until everything is combined, making sure not to overmix so that my muffins stay light and fluffy.
6. Prepare the Cream Cheese Filling:
In another bowl, I’ll beat the softened cream cheese until smooth. Then, I’ll add the sugar, egg, and vanilla extract, mixing until it’s creamy and well blended.
7. Assemble the Muffins:
Here comes the fun part! I’ll fill each muffin cup about halfway with the pumpkin batter. Then, I’ll spoon about 1 tablespoon of the cream cheese filling right into the center of each muffin cup. After that, I’ll top them off with the remaining pumpkin batter, filling the cups nearly to the top.
8. Optional Swirling:
If I’m feeling a bit fancy, I’ll swirl a knife through the batter in each muffin to create a marbled effect. This makes it look extra special!
9. Bake the Muffins:
I’ll pop the muffin pan into the oven and bake for 22-26 minutes. I know they’re done when a toothpick inserted near the edge comes out clean (but not when I poke the cream cheese center!).
10. Cool and Enjoy:
Once they’re baked, I’ll let them cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely. Finally, I can serve them warm or at room temperature and enjoy every delicious bite! If there are leftovers, I’ll store them in an airtight container in the fridge for up to 3 days.
Enjoy your pumpkin cheesecake muffins with a creamy, tangy center that’s sure to impress!

Can I Use Fresh Pumpkin Instead of Canned?
Absolutely! If you prefer using fresh pumpkin, simply cook and puree it until smooth. You’ll need about 1 ¾ cups of fresh puree, making sure to remove excess moisture for the best texture.
How Can I Make These Muffins Gluten-Free?
You can substitute the all-purpose flour with a gluten-free flour blend. Just make sure it contains xanthan gum or add a teaspoon of it yourself for better texture!
Can I Reduce the Sugar in the Recipe?
Yes, you can reduce the sugar by up to ¼ cup without significantly affecting the texture. If you like, you can also use a sugar substitute that measures cup-for-cup like erythritol or stevia.
How Do I Store Leftover Muffins?
Store any leftover muffins in an airtight container at room temperature for about 2 days. For longer storage, they can be refrigerated for up to 3 days or frozen for up to 3 months. Just thaw them overnight in the fridge before enjoying!