Ever had one of those mornings where you wake up craving something that feels like autumn wrapped in a paper liner? That’s exactly what these Pumpkin Cream Cheese Muffins deliver. They’re not just muffins – they’re what happens when pumpkin spice and tangy cream cheese have a beautiful bakery love affair.
The first time I made these for my family, the kitchen filled with warm spices, and they disappeared faster than I could say “save me one!” Trust me, you’re about to discover your new fall baking obsession.
Why This Recipe is Awesome

What makes these Pumpkin Cream Cheese Muffins special isn’t just the perfect balance of spiced pumpkin batter and creamy cheesecake-like filling – it’s how they bring together the best of two worlds. The muffin itself is incredibly moist thanks to the pumpkin, with a tender crumb that stays fresh for days (though they rarely last that long!). Unlike many bakery versions that go heavy on sugar and light on actual pumpkin flavor, these muffins let the natural earthiness of pumpkin shine through, complemented by – not overwhelmed by – the warm spice blend.
The cream cheese center adds a luxurious surprise that elevates these from “just another pumpkin muffin” to something truly crave-worthy. As someone who’s tested dozens of pumpkin recipes over the years, I can confidently say this one hits the sweet spot between impressive enough for company and easy enough for a random Tuesday morning.
Equipment needed: Muffin tin, paper liners, mixing bowls, electric mixer, cooling rack

Pumpkin Cream Cheese Muffins
Ingredients
- For the Muffins:
- 1¾ cups all-purpose flour
- 1 tablespoon pumpkin pie spice
- 1 teaspoon baking soda
- ½ teaspoon salt
- 1 15 oz can pumpkin puree (not pumpkin pie filling)
- 1 cup granulated sugar
- ½ cup packed brown sugar
- 2 large eggs room temperature
- ½ cup vegetable oil
- 1 teaspoon vanilla extract
- For the Cream Cheese Filling:
- 8 oz cream cheese softened (full-fat works best)
- ¼ cup granulated sugar
- 1 large egg yolk
- 1 teaspoon vanilla extract
- Optional Topping:
- ½ cup chopped pecans or walnuts
- 2 tablespoons turbinado sugar sugar in the raw
Instructions
- Preheat your oven to 350°F (175°C) and line a standard 12-cup muffin tin with paper liners. Lightly spray the liners with cooking spray to prevent sticking.
- Prepare the cream cheese filling by beating the softened cream cheese with ¼ cup sugar until smooth and fluffy, about 2 minutes. Add the egg yolk and 1 teaspoon vanilla, mixing until just combined. Set aside.
- In a medium bowl, whisk together the flour, pumpkin pie spice, baking soda, and salt until well combined.
- In a large bowl, combine the pumpkin puree, granulated sugar, and brown sugar, mixing until smooth. Add the eggs one at a time, then pour in the oil and vanilla, mixing thoroughly after each addition.
- Gently fold the dry ingredients into the pumpkin mixture using a rubber spatula, stirring just until no flour streaks remain. Be careful not to overmix, which can make the muffins tough.
- Fill each muffin cup about ⅔ full with the pumpkin batter. This ensures room for the cream cheese filling and proper rising.
- Add a generous tablespoon of cream cheese filling to the center of each muffin. You can use the back of a spoon to slightly press it into the batter.
- If using the optional topping, combine the chopped nuts and turbinado sugar in a small bowl, then sprinkle over each muffin.
- Bake for 22-25 minutes until a toothpick inserted into the pumpkin part (not the cream cheese) comes out with just a few moist crumbs. The tops should spring back when lightly touched.
- Allow the muffins to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely. The cream cheese center will be quite soft when warm but will firm up as they cool.
Notes
- For a more pronounced spice flavor, add ¼ teaspoon of ground cloves or ginger to the dry ingredients.
- These muffins stay fresh at room temperature in an airtight container for up to 2 days, but should be refrigerated after that due to the cream cheese filling.
- The muffins freeze beautifully! Wrap individually in plastic wrap, then store in a freezer bag for up to 3 months. Thaw overnight in the refrigerator.
- Make sure your cream cheese is truly at room temperature for the smoothest filling without lumps.
- If you don’t have pumpkin pie spice on hand, make your own with 1½ teaspoons cinnamon, ½ teaspoon nutmeg, ¼ teaspoon ginger, and ¼ teaspoon allspice.
Calories & Nutritional Info
- Calories: Approximately 320 calories per muffin
- Protein: 5g per muffin
- Carbohydrates: 42g per muffin
- Fat: 15g per muffin
- Contains: Dairy, eggs, wheat (gluten)
- Not suitable for: Vegan or dairy-free diets without modifications
Common Mistakes to Avoid
- Using pumpkin pie filling instead of puree – they’re not the same! Pie filling has added sweeteners and spices that will throw off the recipe.
- Overmixing the batter – this develops gluten and leads to tough, dense muffins. Mix just until ingredients are incorporated.
- Not allowing cream cheese to soften properly – cold cream cheese will create lumps in your filling.
- Filling the muffin cups too full – this causes them to overflow during baking and creates flat tops instead of nice domes.
- Testing doneness in the cream cheese center – always check the pumpkin part of the muffin, as the cream cheese filling will remain soft.
Alternatives & Substitutions
- Gluten-free option: Substitute a 1:1 gluten-free flour blend. The texture may be slightly different, but still delicious.
- Reduce sugar: You can decrease the granulated sugar to ¾ cup without significantly affecting the texture.
- Oil alternatives: Melted coconut oil or melted butter can replace vegetable oil for a different flavor profile.
- Dairy-free: Use dairy-free cream cheese alternative, though the filling may have a slightly different consistency.
- Add-ins: Fold ½ cup chocolate chips into the batter for a sweeter treat, or add ¼ cup finely chopped crystallized ginger for a spicy kick.
- Mini muffins: Reduce baking time to 15-18 minutes for bite-sized treats (makes approximately 36).
FAQs
Can I make these muffins ahead of time?
Absolutely! These Pumpkin Cream Cheese Muffins actually taste even better the next day when the flavors have had time to meld. Store at room temperature for 1-2 days or refrigerate for up to 5 days.
Why did my cream cheese filling sink to the bottom?
This typically happens if your batter is too thin. Make sure you’re measuring flour correctly (spoon and level, don’t scoop) and that your pumpkin puree isn’t too watery. Blotting excess moisture from the puree with paper towels can help.
Can I use homemade pumpkin puree?
Yes! Just make sure it’s drained well, as homemade puree tends to be wetter than canned. You might need to add an extra 1-2 tablespoons of flour to compensate.
My muffins didn’t dome up nicely. What went wrong?
Two common culprits: your oven temperature might be too low (consider using an oven thermometer), or your baking soda might be expired. For beautifully domed muffins, make sure your oven is fully preheated before baking.
Can I turn this into a loaf instead of muffins?
Definitely! Pour half the batter into a greased 9×5 loaf pan, add the cream cheese filling in a line down the center, then top with remaining batter. Bake at 350°F for 60-70 minutes or until a toothpick comes out clean.
Final Thoughts
These Pumpkin Cream Cheese Muffins aren’t just a recipe – they’re a little moment of autumn joy you can create any time of year. There’s something magical about breaking open a warm muffin and finding that creamy center waiting inside. Whether they become your signature fall breakfast or your way of bringing cozy vibes to an ordinary morning, I hope they bring as much happiness to your kitchen as they have to mine.