These Pumpkin Cheesecake Muffins are a perfect treat for fall! Packed with warm pumpkin spice flavor and a creamy cheese filling, they are soft and oh-so-delicious.
You’ll love how these muffins fill your kitchen with a sweet smell while baking. They are so good; I might just have to hide a few from my family! 😄
These muffins are easy to whip up and make a great snack or breakfast. I enjoy them warm with a cup of coffee—it’s the best way to start the day!
Key Ingredients & Substitutions
Pumpkin Puree: This is the star of the show! You can use canned pumpkin puree or make your own by cooking and blending fresh pumpkin. If you need a substitute, look for mashed sweet potatoes or butternut squash.
Spices: A mix of cinnamon, nutmeg, ginger, and cloves adds warmth. If you’re out of any spice, you can use pumpkin pie spice as a perfect alternative, giving you all those flavors in one scoop!
All-Purpose Flour: This gives the muffins structure. If you’re gluten-free, you can use a 1:1 gluten-free flour blend, and it should work just as well.
Cream Cheese: For the filling, use full-fat cream cheese for a rich flavor. If you want a lighter option, you can use low-fat cream cheese or even a dairy-free version, like cashew cheese.
How Do I Get the Cream Cheese Filling Just Right?
Getting the cream cheese filling smooth and creamy is essential for these muffins. Here’s how to master it:
- Make sure your cream cheese is at room temperature; this helps it mix easily.
- Beat the cream cheese and sugar until smooth before adding the egg. This creates a creamy texture.
- Don’t overmix after adding the egg. Mix just until combined to keep the filling light.
Swirling the cream cheese filling with the pumpkin batter not only looks beautiful but also ensures every bite has that lovely creamy taste. Enjoy your baking! 🍂

How to Make Pumpkin Cheesecake Muffins With Cream Cheese Filling
Ingredients You’ll Need:
For the Pumpkin Muffin Batter:
- 1 ½ 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
- 1 cup pumpkin puree (canned or fresh)
- ½ cup granulated sugar
- ½ cup light brown sugar, packed
- ⅓ cup vegetable oil (or melted butter)
- 2 large eggs
- 1 teaspoon vanilla extract
For the Cream Cheese Filling:
- 8 ounces cream cheese, softened
- ⅓ cup granulated sugar
- 1 large egg
- 1 teaspoon vanilla extract
How Much Time Will You Need?
This delightful recipe calls for about 15 minutes of prep time, plus 20-25 minutes of baking. After baking, allow the muffins to cool for about 5 minutes in the pan before transferring to a wire rack to cool completely. Total time is around 45-50 minutes until you’re ready to enjoy these tasty treats!
Step-by-Step Instructions:
1. Preheat Oven and Prepare Muffin Tin:
Start by preheating your oven to 350°F (175°C). Prepare a 12-cup muffin tin by lining it with paper liners or greasing it with non-stick spray to ensure easy removal later.
2. Make the Cream Cheese Filling:
In a medium bowl, mix the softened cream cheese and granulated sugar with a hand mixer until you achieve a smooth and creamy consistency. Add in the egg and vanilla extract, and continue to mix until it’s fully combined and smooth. Set this mixture aside; it will be the delicious filling!
3. Prepare the Pumpkin Muffin Batter:
In a large bowl, whisk together the dry ingredients: flour, baking powder, baking soda, cinnamon, nutmeg, ginger, cloves, and salt.
In another bowl, combine the pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla extract. Whisk this mixture well until it is smooth and fully combined.
4. Combine Wet and Dry Ingredients:
Now, take the wet pumpkin mixture and add it to the bowl of dry ingredients. Gently fold the two mixtures together using a spatula, being careful not to overmix. You want to combine them just until no flour streaks remain!
5. Assemble the Muffins:
Pour half of the pumpkin batter into each muffin cup (about halfway full). Then, take about 1 tablespoon of the cream cheese filling and spoon it on top of the pumpkin batter in each cup.
Use the remaining pumpkin batter to fill the cups about ¾ full. With a knife or skewer, gently swirl the cream cheese filling into the batter on top to create a lovely marbled effect!
6. Bake:
Slide the muffin tin into your preheated oven and bake for 20 to 25 minutes. To check if they’re done, insert a toothpick into the muffin (avoiding the cream cheese swirl). If it comes out clean, they are ready to be taken out!
7. Cool and Serve:
After baking, allow the muffins to cool in the pan for about 5 minutes. Carefully transfer them to a wire rack to cool completely. Enjoy them warm or at room temperature for an absolutely delicious experience!
These Pumpkin Cheesecake Muffins with their creamy swirls are perfect for cozy fall breakfasts or a delightful snack anytime. Enjoy every bite!

Can I Use Fresh Pumpkin Instead of Canned Puree?
Absolutely! If you prefer using fresh pumpkin, just make sure to roast and puree it until smooth. About 1 medium-sized pumpkin will yield enough puree for this recipe. Just be sure to drain any excess moisture for the perfect muffin texture!
How Should I Store Leftover Muffins?
Store any leftover muffins in an airtight container at room temperature for up to 3 days. If you want to keep them longer, you can freeze them by wrapping each muffin in plastic wrap and placing them in a freezer-safe bag. They can be stored in the freezer for up to 3 months!
Can I Substitute the Cream Cheese Filling?
Yes! If you want a lighter filling, you can use Greek yogurt or a dairy-free alternative like cashew cream. Just ensure it has a thick consistency for the best results. Adjust the sweetness accordingly to suit your taste!
What if My Batter is Too Thick?
If your batter seems too thick, don’t worry! You can add a splash of milk or a bit more oil to achieve the desired consistency. Just mix gently until it reaches a nicer, pourable batter without overmixing!


