When autumn makes its grand entrance, the craving for warm, spiced baked goods is undeniable. At the top of that list is the perfect marriage of flavors: tangy, sweet cream cheese swirled into a moist, spiced pumpkin muffin. This recipe for Pumpkin Cream Cheese Muffins is the ultimate fall indulgence. It combines the earthy comfort of pumpkin with the rich, creamy surprise of a cheesecake-like filling, creating a treat that feels truly special. While a savory dish like a cozy one-pot creamy pumpkin pasta satisfies our craving for a hearty fall meal, these muffins are a sweet counterpart that’s perfect for breakfast or an afternoon snack. They elevate the classic muffin, much like how Greek yogurt blueberry protein muffins add a wholesome twist to a familiar favorite.
Ingredients for Your Muffins
This recipe has two key components: the tangy cream cheese filling and the perfectly spiced pumpkin muffin batter. Don’t be intimidated; both are incredibly simple to whip up.
For the Cream Cheese Filling:
- 8 ounces cream cheese, softened to room temperature
- 1/3 cup granulated sugar
- 1 large egg yolk
- 1 teaspoon vanilla extract
For the Pumpkin Muffins:
- 1 ¾ cups all-purpose flour
- 1 teaspoon baking soda
- 2 teaspoons pumpkin pie spice (or a mix of cinnamon, nutmeg, and ginger)
- ½ teaspoon salt
- 2 large eggs
- 1 cup granulated sugar
- ½ cup packed light brown sugar
- 1 cup pumpkin puree
- ½ cup vegetable oil
- Optional: Coarse sugar or a streusel topping for sprinkling

Step-by-Step Instructions
Assembling these Pumpkin Cream Cheese Muffins is a fun process of layering batter and filling to create that beautiful swirl.
- Preheat and Prepare: Preheat your oven to 400°F (200°C). Line a 12-cup muffin tin with paper liners.
- Make the Cream Cheese Filling: In a medium bowl, use an electric mixer to beat the softened cream cheese and sugar until smooth and creamy. Beat in the egg yolk and vanilla extract until just combined. Set aside.
- Combine Dry Muffin Ingredients: In a large bowl, whisk together the flour, baking soda, pumpkin pie spice, and salt.
- Combine Wet Muffin Ingredients: In a separate bowl, whisk together the eggs, granulated sugar, and brown sugar. Add the pumpkin puree and vegetable oil and whisk until everything is smooth.
- Mix the Muffin Batter: Pour the wet ingredients into the dry ingredients and gently fold with a spatula until just combined. Do not overmix.
- Assemble the Muffins: Add about 2 tablespoons of the pumpkin batter to the bottom of each muffin liner. Top that with a heaping tablespoon of the cream cheese filling. Finish by dividing the remaining pumpkin batter over the cream cheese filling.
- Create the Swirl: Use a toothpick or the tip of a knife to gently swirl the layers together. A simple figure-eight motion works well. Sprinkle with coarse sugar if desired.
- Bake: Bake for 18-20 minutes, or until a toothpick inserted into the pumpkin muffin part comes out with moist crumbs attached.
- Cool Completely: Let the muffins cool in the tin for 10 minutes before transferring them to a wire rack to cool completely. The filling will set as it cools.
Pro Tips for Perfect Muffins
To ensure your Pumpkin Cream Cheese Muffins turn out perfectly every time, keep these tips in mind. First, using room temperature cream cheese and egg yolk is crucial for a smooth, lump-free filling. Second, be careful not to overmix the muffin batter, as this can lead to tough muffins. For the best flavor, use your own blend of spices or a quality store-bought version. You can even make your own Homemade Pumpkin Pie Spice with this direct recipe from Allrecipes. Finally, let the muffins cool completely before enjoying them, as this allows the cream cheese filling to set properly.
More Fall Baking Ideas
If this recipe ignites your passion for fall baking, there are many other seasonal treats to try. For a stunning centerpiece that’s perfect for a weekend project, this chai apple babka recipe weaves together the flavors of sweet apple and aromatic chai spices in a beautiful braided loaf. Other classic ideas include a simple apple crumble, a pear and almond tart, or a batch of soft molasses cookies.

Conclusion
These Pumpkin Cream Cheese Muffins are more than just a recipe; they are a celebration of autumn in a single bite. The delightful contrast between the spiced pumpkin cake and the creamy, tangy filling makes them an unforgettable treat that feels both comforting and indulgent. They are perfect for sharing with family, bringing to a fall gathering, or simply enjoying with a hot cup of coffee on a crisp morning. As the season progresses, these comforting bakes pave the way for other delightful treats, like festive Christmas snacks. We hope this becomes your new favorite fall tradition.