These Pumpkin Cheesecake Muffins are a tasty treat that combines pumpkin flavor with a sweet cream cheese filling. They’re perfect for a cozy morning or a delightful snack!
It’s like a little dessert in a muffin form! I love how easy they are to make, and they fill the kitchen with a warm, comforting smell. Enjoy them fresh and watch them disappear!
Key Ingredients & Substitutions
All-Purpose Flour: This is a staple for muffins. If you’re gluten-free, try a 1:1 gluten-free flour blend. It works great for texture without changing the taste!
Canned Pumpkin Puree: Canned pumpkin is convenient but you can use fresh pumpkin too. Just roast and mash it, which gives a little more flavor. But, make sure to remove excess moisture!
Granulated and Brown Sugar: Both add sweetness and richness. If you want to cut down on sugar, use a sugar substitute like Stevia or coconut sugar. Just check conversion ratios on the package!
Cream Cheese: Full-fat cream cheese gives the best taste and texture. Light cream cheese can be used, but it may be less rich. You can even swap in mascarpone for something a bit different!
How Do I Get the Perfect Swirl in My Muffins?
Creating that beautiful swirl takes a little care but is totally worth it! Follow these tips for the best results:
- **Layering:** Start by adding the pumpkin batter first, then the cream cheese filling, and top it off with more pumpkin batter. This layering helps with the swirl.
- **Gentle Swirling:** Use a toothpick or skewer to gently twirl the batter. Don’t overdo it—just a few turns will create a nice marbled look!
- **Lovingly Bake:** Watch the time! Don’t let them bake too long or the cream cheese filling might overcook and lose its yummy texture.
With these tips, your muffins will look as good as they taste! Enjoy the baking process!

How to Make Pumpkin Cheesecake Muffins With Cream Cheese Filling
Ingredients You’ll Need:
For the Pumpkin Muffin Batter:
- 1 3/4 cups (220g) all-purpose flour
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon salt
- 1 tablespoon ground cinnamon
- 1/2 teaspoon ground ginger
- 1/4 teaspoon ground nutmeg
- 1/4 teaspoon ground cloves
- 1/2 cup (100g) granulated sugar
- 1/2 cup (110g) brown sugar, packed
- 2 large eggs
- 1 cup (240ml) canned pumpkin puree
- 1/3 cup (80ml) vegetable oil
- 1 teaspoon vanilla extract
For the Cream Cheese Filling:
- 8 oz (225g) cream cheese, softened
- 1/4 cup (50g) granulated sugar
- 1 large egg
- 1/2 teaspoon vanilla extract
How Much Time Will You Need?
This recipe will take about 15 minutes to prepare and 20-25 minutes to bake. After baking, allow the muffins to cool for about 5 minutes in the pan before transferring them to a wire rack. In total, plan for about 1 hour to make this delicious treat!
Step-by-Step Instructions:
1. Prepare Oven and Pan:
Start by preheating your oven to 350°F (175°C). While it heats up, line a 12-cup muffin tin with paper liners or grease it well to prevent sticking.
2. Make the Cream Cheese Filling:
In a medium bowl, beat the softened cream cheese and sugar together until the mixture is smooth and creamy. Then, add in the egg and vanilla extract, mixing until well combined. Set this creamy filling aside for later.
3. Mix the Dry Ingredients:
In a large mixing bowl, whisk together the all-purpose flour, baking powder, baking soda, salt, and spices (cinnamon, ginger, nutmeg, and cloves). This ensures that your muffins rise well and have a great flavor!
4. Mix the Wet Ingredients:
In a separate bowl, combine granulated sugar, brown sugar, eggs, pumpkin puree, vegetable oil, and vanilla extract. Whisk these together until the mixture is smooth.
5. Combine Wet and Dry Ingredients:
Pour the wet ingredients into the dry ingredients and gently stir them together. Be careful not to overmix; just stir until everything is combined. A few lumps are okay!
6. Fill Muffin Cups:
Spoon about 2 tablespoons of pumpkin batter into each muffin cup. Next, add about 1 tablespoon of the cream cheese filling on top of the pumpkin batter in each cup. Finally, cover this with the remaining pumpkin batter until the cups are about 2/3 full.
7. Create Swirls:
To make those pretty swirls, use a toothpick or skewer and gently swirl the cream cheese filling into the pumpkin batter. Just a few soft twists will do to create a marbled effect!
8. Bake:
Place the muffin tin in the preheated oven and bake for 20-25 minutes. Check if they’re done by inserting a toothpick near the edge; it should come out clean (avoid the cream cheese center).
9. Cool and Serve:
Once baked, remove the muffins from the oven and let them cool in the muffin tin for about 5 minutes. After that, transfer them to a wire rack to cool completely. Enjoy your delicious pumpkin cheesecake muffins warm or at room temperature!
These muffins are perfect for a cozy morning or as a delightful afternoon snack. Enjoy the flavors of fall!

Can I Use Homemade Pumpkin Puree Instead of Canned?
Absolutely! If you have fresh pumpkin, just roast it, scoop out the flesh, and blend it until smooth. Make sure to drain any excess moisture to maintain the right texture.
Can I Substitute the Cream Cheese Filling with Something Else?
Yes, you can! If you’re looking for a lighter option, try using Greek yogurt or a ricotta filling. Just blend it with a bit of sugar and an egg for creaminess.
How Should I Store Leftover Muffins?
Store any leftover muffins in an airtight container at room temperature for up to 3 days. For longer storage, wrap them tightly in plastic wrap and freeze for up to 2 months. Thaw at room temperature when you’re ready to enjoy!
Can I Make These Muffins Vegan?
Definitely! You can substitute eggs with flax eggs (1 tablespoon flaxseed meal mixed with 2.5 tablespoons water per egg) and use a plant-based cream cheese alternative. Also, make sure your sugars are vegan-friendly!


