Name: Pumpkin Cream Cheese Muffins
Prep time: 25 min
Cook time: 22 min
Total time: 47 min

Pumpkin Cream Cheese Muffins

There’s something about pumpkin season that makes baking feel extra special. As these Pumpkin Cream Cheese Muffins bake, the kitchen fills with the warm aroma of cinnamon and pumpkin spice.

The buttery crumb topping turns perfectly golden, and when you break one open, you’ll find a smooth, creamy cream cheese center tucked inside every soft, fluffy muffin.

I come back to this recipe every fall because it has everything I love in a homemade muffin. The pumpkin keeps each bite incredibly moist, while the cheesecake filling adds just the right amount of richness.

The cinnamon streusel brings a buttery crunch that makes these muffins taste like they came straight from a neighborhood bakery.

Bake a batch for a cozy breakfast, an afternoon coffee break, or an easy dessert. They’re just as delicious warm from the oven as they are the next day.

And because they freeze beautifully, you can always have a homemade fall treat ready whenever the craving strikes.

Why You’ll Love This Recipe

These Pumpkin Cream Cheese Muffins have become one of my favorite fall bakes, and it’s easy to see why.

A creamy cheesecake surprise. Every muffin hides a smooth cream cheese filling that makes each bite rich and satisfying.
Soft, tender, and full of pumpkin flavor. Pumpkin puree keeps the muffins wonderfully moist while adding the cozy taste of fall.
Warm fall spices in every bite. Cinnamon and pumpkin pie spice create a comforting flavor that feels right at home on crisp autumn days.
A buttery crumb topping. The cinnamon streusel adds just the right amount of sweetness and a lightly crisp finish.
Perfect for any time of day. Enjoy them for breakfast, with an afternoon coffee, or as a simple dessert after dinner.
Easy to make ahead. These muffins stay fresh for several days and freeze well, making them perfect for meal prep or sharing with family and friends.

Ingredients You Will Need

These Pumpkin Cream Cheese Muffins come together with three simple components: a buttery cinnamon crumb topping, a soft pumpkin muffin batter, and a creamy cheesecake filling. Here’s what each ingredient does.

For the Crumb Topping

Brown Sugar – Adds a rich caramel-like sweetness and helps create a crisp, golden streusel.
Ground Cinnamon – Gives the topping a warm, cozy spice that pairs perfectly with pumpkin.
Unsalted Butter – Melted butter binds the topping together and creates those delicious buttery crumbs.
All-Purpose Flour – Forms the crumbly texture that bakes into a lightly crisp topping.

For the Pumpkin Muffins

All-Purpose Flour – Creates the structure for soft, fluffy muffins.
Baking Powder & Baking Soda – Work together to help the muffins rise with tall, bakery-style tops.
Salt – Balances the sweetness and enhances the pumpkin and spice flavors.
Ground Cinnamon – Adds classic fall warmth throughout every bite.
Pumpkin Pie Spice – A blend of cozy spices that gives the muffins their signature autumn flavor.
Brown Sugar – Adds moisture and a subtle caramel flavor.
Granulated Sugar – Sweetens the batter while helping create a tender crumb.
Eggs – Provide structure and help bind all the ingredients together.
Pumpkin Purée – The star ingredient that keeps the muffins incredibly moist and full of pumpkin flavor.
Vegetable Oil – Makes the muffins soft and tender. Melted coconut oil works just as well.
Milk – Adds moisture and helps create a smooth batter.
Vanilla Extract – Rounds out the flavors with a touch of sweetness.

For the Cream Cheese Filling

Cream Cheese – Creates a rich, smooth cheesecake-style center in every muffin.
Egg Yolk – Helps the filling bake into a creamy, silky texture.
Vanilla Extract – Adds a subtle sweetness and complements the cream cheese.
Granulated Sugar – Sweetens the filling without overpowering the pumpkin flavors.

How to Make Pumpkin Cream Cheese Muffins

Step 1: Start by preparing the muffin pan and oven. Preheat your oven to 425°F (218°C) and line a 12-count muffin pan with cupcake liners or spray it with nonstick cooking spray. Since this recipe makes 12–14 muffins, prepare an additional pan if needed.

Step 2: Make the crumb topping first. Combine the brown sugar, cinnamon, and melted butter in a small bowl, then gently mix in the flour with a fork until the mixture forms coarse crumbs. Set the topping aside while you prepare the muffin batter.

Step 3: Prepare the pumpkin muffin batter. In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice. In a separate bowl, mix the brown sugar, granulated sugar, eggs, pumpkin puree, oil, milk, and vanilla extract until smooth.

Step 4: Add the wet ingredients to the dry ingredients and gently stir until just combined. Avoid overmixing the batter to keep the muffins soft and tender.

Step 5: Make the cream cheese filling. Beat the softened cream cheese until smooth and creamy, then mix in the egg yolk, vanilla extract, and sugar until fully combined.

Step 6: Assemble the muffins. Add a heaping tablespoon of pumpkin batter into each muffin cup, followed by a spoonful of cream cheese filling. Cover with another layer of pumpkin batter until the cups are filled to the top. Sprinkle the crumb topping over each muffin and gently press it down.

Step 7: Bake the muffins at 425°F (218°C) for 5 minutes, then reduce the oven temperature to 350°F (177°C) without removing the muffins. Continue baking for another 15–17 minutes, until the muffins are fully baked and the tops are golden.

Step 8: Allow the muffins to cool in the pan for at least 10 minutes before serving. Enjoy them warm, or let them cool completely before storing.

Step 9: Store any leftovers in an airtight container at room temperature for up to 2 days, or refrigerate them for up to 1 week. For longer storage, freeze the muffins for up to 3 months and thaw before enjoying.

Pumpkin Cream Cheese Muffins

These Pumpkin Cream Cheese Muffins pair warmly spiced pumpkin batter with a rich cream cheese center for a bakery-style treat that's perfect for fall. A buttery cinnamon crumb topping adds a delicious crunchy finish, making these muffins ideal for breakfast, brunch, or an afternoon snack.

Print Pin

Course: Breakfast, Dessert

Cuisine: American

Keyword: Pumpkin Cream Cheese Muffins

Prep Time: 25

Cook Time: 22

Total Time: 47

Servings: muffins

Notes

Ingredients

Crumb Topping

1/3 cup (67g) packed light or dark brown sugar
1 teaspoon ground cinnamon
1/4 cup (4 Tbsp; 56g) unsalted butter, melted
2/3 cup (84g) all-purpose flour

Pumpkin Muffins

1 and 3/4 cups (219g) all-purpose flour (spooned & leveled)
1 teaspoon baking powder
1 teaspoon baking soda
1/2 teaspoon salt
2 teaspoons ground cinnamon
1 teaspoon store-bought or homemade pumpkin pie spice*
1/2 cup (100g) packed light or dark brown sugar
1/2 cup (100g) granulated sugar
2 large eggs, at room temperature
1 cup (227g) canned pumpkin puree
1/2 cup (120ml) vegetable oil (or melted coconut oil)
1/3 cup (80ml) milk
1 teaspoon pure vanilla extract

Cream Cheese Filling

6 ounces (170g) full-fat brick cream cheese, softened to room temperature
1 egg yolk, at room temperature
1/2 teaspoon pure vanilla extract
3 Tablespoons (36g) granulated sugar

Instructions

Preheat the oven to 425°F (218°C). Grease a 12-cup muffin pan with nonstick spray or line it with paper liners. Since this recipe yields 12–14 muffins, prepare a second pan or bake the remaining batter in a separate batch if needed.
Prepare the crumb topping by stirring together the brown sugar, cinnamon, and melted butter in a small bowl. Add the flour and gently combine with a fork until coarse crumbs form. Be careful not to overmix—the mixture should stay crumbly rather than turning into a paste. Set aside.
To make the pumpkin batter, whisk together the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice in a large bowl.
In another bowl, whisk the brown sugar, granulated sugar, eggs, pumpkin puree, oil, milk, and vanilla extract until smooth. Add the wet mixture to the dry ingredients and stir just until everything is incorporated. Do not overmix.
For the cream cheese filling, beat the softened cream cheese with a handheld or stand mixer fitted with a paddle or whisk attachment until smooth. Add the egg yolk, vanilla extract, and sugar, then beat until fully blended.
Fill each muffin cup with 1 heaping Tablespoon of pumpkin batter. Add approximately 1 spoonful (not quite a full Tablespoon) of the cream cheese filling, then top with another heaping Tablespoon of pumpkin batter, or enough batter to fill each cup to the top. It's perfectly fine if a little of the filling is visible. Sprinkle the crumb topping over each muffin and gently press it into the batter so it stays in place while baking.
Bake for 5 minutes at 425°F (218°C). Without opening the oven, reduce the temperature to 350°F (177°C) and continue baking for 15–17 minutes, for a total baking time of approximately 20–22 minutes.
Let the muffins cool in the pan for at least 10 minutes before removing and serving.
Store leftover muffins in an airtight container at room temperature for up to 2 days, or refrigerate for up to 1 week.

Notes

Freezing: Freeze the baked muffins for up to 3 months. Thaw overnight in the refrigerator and warm in the microwave before serving if desired.
Pumpkin Pie Spice: Use store-bought or homemade pumpkin pie spice. If unavailable, substitute 1/4 teaspoon each of ground ginger, ground nutmeg, ground cloves, and ground allspice, in addition to the 2 teaspoons ground cinnamon listed in the recipe.
Why Start at a Higher Temperature? Baking the muffins at a higher temperature for the first 5 minutes helps them rise quickly, creating tall, domed tops. Lowering the oven temperature afterward allows the centers to finish baking evenly without overbrowning.

Save

1. Can I use fresh pumpkin instead of canned pumpkin puree?

Yes, you can use homemade pumpkin puree in this recipe. Just make sure it has a similar thick consistency to canned pumpkin so the muffins stay soft, moist, and bake properly.

2. Why did my cream cheese filling sink or disappear into the muffins?

A little sinking is completely normal, but to keep the filling nicely layered, make sure the cream cheese mixture is thick and the muffin batter is added around it carefully. Avoid overfilling the cups with the cream cheese mixture.

3. Can I make these muffins without the crumb topping?

Absolutely. The crumb topping adds extra sweetness and texture, but the muffins are still delicious without it. You can bake them as simple pumpkin cream cheese muffins if you prefer.

4. Do I need to refrigerate pumpkin cream cheese muffins?

Yes, because of the cream cheese filling, these muffins are best stored in the refrigerator. Keep them covered in an airtight container, and they’ll stay fresh for up to 1 week.

5. How can I get tall bakery-style muffin tops?

The secret is the two-temperature baking method. Starting the muffins at 425°F (218°C) helps create a quick rise, then lowering the temperature allows the centers to bake evenly while keeping the tops beautifully domed.