These Pumpkin Cheesecake Muffins are a cozy treat for any time of year! Soft pumpkin muffins with a sweet cream cheese filling make them irresistible.
Who can say no to the mix of pumpkin spice and a creamy surprise inside? I love serving them warm with a cup of coffee—it’s like a hug on a plate!
Key Ingredients & Substitutions
Pumpkin Puree: Canned pumpkin is easy and convenient. If you have fresh pumpkin, you can roast and puree it. This adds a sweeter, more concentrated flavor.
Spices: Cinnamon and nutmeg are classic for pumpkin flavor. If you’re out of ground ginger or cloves, using more cinnamon can work in a pinch! You can also try pumpkin pie spice for a quick substitute.
Flour: All-purpose flour is standard, but if you need a gluten-free option, swap in a 1:1 gluten-free flour blend. I’ve had great results with that!
Cream Cheese: Look for full-fat cream cheese for richness. If you want a lighter option, you can use low-fat cream cheese, but the texture may be a bit different.
Sugar: Feel free to adjust the sugars as needed. Using coconut sugar or a sugar substitute can work, just be mindful of the sweetness level.
What’s the Best Way to Mix the Batter Without Overdoing It?
Mixing the batter carefully is key to tender muffins. Start by whisking together your dry ingredients until blended. When adding them to the wet pumpkin mixture, use a spatula to gently fold them in.
- Mix until *just* combined; some lumps are okay.
 - Over-mixing can lead to dense muffins, so be light-handed!
 - During assembly, when you spoil the cream cheese, ensure it’s airy; otherwise, it will sink to the bottom.
 

Pumpkin Cheesecake Muffins With Cream Cheese Filling
Ingredients
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 teaspoon ground cinnamon
 - 1/2 teaspoon ground ginger
 - 1/4 teaspoon ground nutmeg
 - 1/4 teaspoon ground cloves
 - 1 cup (225g) canned pumpkin puree
 - 1/2 cup (100g) granulated sugar
 - 1/2 cup (100g) light brown sugar, packed
 - 1/2 cup (120ml) vegetable oil or melted unsalted butter
 - 2 large eggs
 - 1 teaspoon vanilla extract
 
For the Cream Cheese Filling:
- 8 oz (225g) cream cheese, softened
 - 1/4 cup (50g) granulated sugar
 - 1 teaspoon vanilla extract
 - 1 large egg yolk
 
Time Needed
This delightful recipe will take about 15 minutes for prep and about 20-25 minutes for baking, plus 5 more minutes to cool. In total, set aside around 40-45 minutes to make these delicious muffins!
Instructions
1. Preheat the Oven:
Start by preheating your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease it well with cooking spray or butter to ensure easy removal.
2. Mix the Dry Ingredients:
In a medium bowl, whisk together the flour, baking powder, baking soda, salt, and all the spices (cinnamon, ginger, nutmeg, and cloves) until they are evenly combined. This step helps the spices to be dispersed throughout the batter.
3. Prepare the Pumpkin Batter:
In a large bowl, combine the pumpkin puree, granulated sugar, brown sugar, vegetable oil (or melted butter), eggs, and vanilla extract. Whisk them together until the mixture is smooth and well combined.
4. Combine Wet and Dry Ingredients:
Gradually add the dry ingredients to the pumpkin mixture, folding gently with a spatula or wooden spoon just until there are no flour streaks. Be careful not to over-mix; a few lumps are totally fine!
5. Make the Cream Cheese Filling:
In a separate bowl, beat the softened cream cheese until it is smooth. Add in the granulated sugar, vanilla extract, and egg yolk, continuing to mix until everything is creamy and well combined.
6. Assemble the Muffins:
To assemble, spoon about 2 tablespoons of pumpkin batter into each muffin cup to cover the bottom. Follow this by adding a generous tablespoon of cream cheese filling on top, and then cover with an additional 2 tablespoons of pumpkin batter until each cup is about 3/4 full.
7. Create Swirls (Optional):
If you’d like, you can create beautiful swirls by using a toothpick or skewer to gently swirl the cream cheese filling into the pumpkin batter. This is not only pretty but adds a lovely touch!
8. Bake the Muffins:
Place the muffin tin in the oven and bake for approximately 20-25 minutes. They are done when a toothpick inserted into the pumpkin muffin part (not the cream cheese swirl) comes out clean, and the tops are slightly golden.
9. Cool and Serve:
Once baked, remove the muffins from the oven and allow them to cool in the pan for about 5 minutes. Then transfer the muffins to a wire rack to cool completely. They can be served warm or at room temperature.
10. Storing the Muffins:
Any leftovers can be stored in an airtight container in the refrigerator for up to 4 days. Enjoy them warm with your favorite cup of coffee or tea!
These moist pumpkin muffins with silky cream cheese filling are perfect for any occasion. Enjoy the fall flavors any time of year!

Can I Substitute Fresh Pumpkin for Canned Pumpkin?
Absolutely! You can use fresh pumpkin. Just roast the pumpkin until tender, scoop out the flesh, and puree it in a food processor until smooth. Make sure it’s properly cooled before adding it to the batter!
How Can I Make These Muffins Gluten-Free?
You can easily make these muffins gluten-free by substituting the all-purpose flour with a 1:1 gluten-free flour blend. Make sure it includes xanthan gum to help mimic the texture of regular flour.
What If I Don’t Have Cream Cheese?
If you’re out of cream cheese, you can use ricotta or mascarpone cheese for a different but delicious filling. Just beat them until smooth and sweeten with a little extra sugar if desired!
How Do I Store & Reheat Leftover Muffins?
Store the cooled muffins in an airtight container in the fridge for up to 4 days. To reheat, simply microwave them for 10-15 seconds or warm them in the oven at 350°F (175°C) for about 5 minutes to refresh their texture!