These soft pumpkin muffins are filled with a creamy, sweet cheese center that makes each bite a joy! Perfect for fall, they smell amazing while baking.
I love having these muffins for breakfast or as a snack with a cozy drink. They never last long at my house—everyone gobbles them up! 🎃🧁
Key Ingredients & Substitutions
All-Purpose Flour: This is the main ingredient for the muffins. If you’re looking for a gluten-free option, try a gluten-free baking blend instead—just check the package for measurements and tips.
Canned Pumpkin Puree: Make sure to use pure pumpkin puree, not pumpkin pie filling. If you have fresh pumpkin, you can cook and puree it as a tasty alternative.
Cream Cheese: This gives the filling its rich flavor. You can swap it out for mascarpone for a different creamy experience, or use a dairy-free cream cheese for a vegan option.
Spices: The cinnamon, nutmeg, cloves, and ginger create a wonderful pumpkin spice flavor. Feel free to adjust the amounts or omit optional spices based on what you have on hand or your taste preferences!
How Do I Make the Cream Cheese Filling Smooth?
Creating a smooth cream cheese filling is key for these muffins. Here’s how you can achieve that:
- Make sure your cream cheese is at room temperature before mixing. This helps it blend easily, avoiding lumps.
- Beat the cream cheese and sugar together first until creamy, then add the egg and vanilla. This sequence helps combine everything well.
Mix just until smooth; over-beating can introduce air, which might affect the texture. Trust me, a creamy filling makes for heavenly muffins!
What’s the Best Way to Assemble the Muffins?
Filling these muffins can feel tricky. Here’s a step-by-step guide to get it right:
- Start by filling each muffin cup with a layer of pumpkin batter—just about a third full.
- Spoon the cream cheese filling right on top of the batter. Avoid touching the edges to prevent overflow.
- Finally, cover the cream cheese with more pumpkin batter until filled about 3/4 full. This layering makes for a delicious surprise inside!
Following these steps will help ensure that each muffin has a delightful balance of flavors. Enjoy your baking! 🧁

How to Make Pumpkin Cream Cheese Filled Muffins
Ingredients You’ll Need:
For the Muffin Batter:
- 1 3/4 cups all-purpose flour
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon salt
- 1 teaspoon ground cinnamon
- 1/2 teaspoon ground nutmeg
- 1/4 teaspoon ground cloves (optional)
- 1/4 teaspoon ground ginger (optional)
- 1 cup canned pumpkin puree
- 1/2 cup granulated sugar
- 1/2 cup brown sugar, packed
- 1/2 cup vegetable or canola oil
- 2 large eggs
- 1 teaspoon vanilla extract
For the Cream Cheese Filling:
- 8 oz cream cheese, softened
- 1/3 cup granulated sugar
- 1 large egg
- 1 teaspoon vanilla extract
For the Cinnamon Streusel Topping:
- 1/2 cup all-purpose flour
- 1/3 cup granulated sugar
- 1/2 teaspoon ground cinnamon
- 1/4 cup unsalted butter, cold and cubed
How Much Time Will You Need?
This recipe will take about 15 minutes to prepare and about 20-25 minutes to bake. Once cooled, your delicious muffins will be ready to enjoy! Make sure to let them cool completely before digging in for the best flavor.
Step-by-Step Instructions:
1. Preheat the Oven:
Start by preheating your oven to 350°F (175°C). This ensures your muffins will bake evenly and rise nicely. Line a muffin tin with paper liners or grease each cup well to prevent sticking.
2. Make the Cinnamon Streusel Topping:
In a small bowl, combine the flour, sugar, and cinnamon. Use a pastry cutter or your fingers to cut in the cold, cubed butter until the mixture looks like coarse crumbs. Set this mixture aside; it will add a delicious crunch to your muffins!
3. Prepare the Cream Cheese Filling:
In a medium bowl, beat together the softened cream cheese, sugar, egg, and vanilla until smooth and creamy. This will create a rich filling that goes beautifully with the pumpkin muffins!
4. Mix the Dry Ingredients:
In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, nutmeg, cloves, and ginger. This combination of spices will give your muffins that warm, autumn flavor.
5. Mix the Wet Ingredients:
In another bowl, whisk together the pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla extract until well combined. This mixture adds moisture and sweetness to your muffins.
6. Combine Wet and Dry Ingredients:
Slowly add the wet ingredient mixture to the dry ingredients. Gently fold them together until just combined—be careful not to overmix; a few lumps are perfectly fine!
7. Assemble the Muffins:
Fill each muffin cup about one-third full with the pumpkin batter. Then add a tablespoon of the cream cheese filling on top of the batter. Finally, cover the cream cheese with more pumpkin batter until each cup is about three-quarters full.
8. Add the Topping:
Sprinkle a generous amount of the streusel topping over each muffin. This will create a delightful crunchy texture once baked!
9. Bake:
Place your muffin tin in the oven and bake for 20-25 minutes. Check for doneness by inserting a toothpick into the muffin (make sure it’s not hitting the cream cheese filling!). It should come out clean or with just a few moist crumbs when they are done.
10. Cool & Serve:
Once baked, let the muffins cool in the pan for about 5 minutes. Then, transfer them to a wire rack to cool completely. These muffins are best enjoyed at room temperature but can also be warmed slightly before serving for added goodness. Enjoy your delicious Pumpkin Cream Cheese Filled Muffins!

Can I Use Fresh Pumpkin Instead of Canned?
Absolutely! You can cook and puree fresh pumpkin for this recipe. Just make sure the puree is smooth and well-drained to avoid extra moisture, which could lead to dense muffins.
How Can I Make These Muffins Healthier?
You can substitute half of the all-purpose flour with whole wheat flour for added fiber. Also, consider reducing the sugar slightly or using a natural sweetener like maple syrup or honey instead—just adjust the liquid content accordingly!
How Should I Store Leftovers?
Store any leftover muffins in an airtight container at room temperature for up to 3 days. For longer storage, you can refrigerate them for up to a week or freeze them for up to 3 months. To reheat, simply warm in the microwave or oven before enjoying.
Can I Add Nuts or Other Mix-ins?
Definitely! Chopped walnuts, pecans, or even chocolate chips make great additions to these muffins. Just fold them into the batter before filling the muffin cups for a delicious twist!