Pumpkin cream cheese muffins pair a tender, warmly spiced pumpkin crumb with a creamy, sweet center that bakes right into the middle. They taste like fall and look like they came from a bakery.

These easy pumpkin cream cheese muffins use one bowl for the batter and a quick mix-in for the filling. If you love pumpkin muffins with cream cheese filling, this bakery style pumpkin cream cheese muffins recipe is the one to bookmark.

Recipe at a Glance

Prep Time	20 minutes
Cook Time	22 minutes
Total Time	42 minutes
Servings	12 muffins
Category	Baking / Breakfast / Snack

Why You’ll Love These Pumpkin Cream Cheese Muffins

Moist, tender crumb with warm pumpkin spice flavor
A creamy cream cheese center in every bite
Simple, no-mixer batter
Great for breakfast, snacks, or fall gatherings
Freezes well for make-ahead mornings

Ingredients You’ll Need

2 cups all-purpose flour
1 teaspoon baking powder, 1 teaspoon baking soda, and ½ teaspoon salt
2 teaspoons pumpkin pie spice
1 cup pumpkin puree (not pie filling)
½ cup packed brown sugar and ¼ cup granulated sugar
½ cup neutral oil, 2 large eggs, ¼ cup milk, and 1 teaspoon vanilla extract
For the filling: 6 ounces softened cream cheese, ¼ cup powdered sugar, and ½ teaspoon vanilla extract

How to Make Pumpkin Cream Cheese Muffins

Preheat the oven to 375°F (190°C) and line a 12-cup muffin pan with paper liners.
Beat the cream cheese, powdered sugar, and vanilla until smooth and set aside.
In a large bowl, whisk the flour, baking powder, baking soda, salt, and pumpkin pie spice.
In a second bowl, whisk the pumpkin, both sugars, oil, eggs, milk, and vanilla, then fold into the dry ingredients until just combined.
Fill each liner halfway, add a tablespoon of cream cheese filling, then top with more batter until about ¾ full.
Bake for 20 to 22 minutes until a toothpick comes out clean from the cake portion, then cool in the pan for 10 minutes.

Tips for the Best Bakery-Style Pumpkin Muffins

Use softened cream cheese so the filling mixes smoothly.
Do not overmix the batter or the muffins will be tough.
Make sure the filling is fully covered with batter to prevent browning.
Rest the batter for 10 minutes for taller muffin tops.
Cool completely before storing to avoid sogginess.

Variations to Try: Pumpkin Muffins with Cream Cheese Filling

Sprinkle cinnamon sugar or pepitas on top before baking.
Fold in ½ cup mini chocolate chips for a sweeter muffin.
Top with a quick maple glaze.
Make mini muffins and bake for 12 to 14 minutes.

How to Store It

Because of the cream cheese filling, store the muffins in an airtight container in the fridge for up to 5 days. Bring to room temperature or warm for 15 seconds in the microwave before eating. Freeze for up to 3 months and thaw overnight.

Frequently Asked Questions

Do pumpkin cream cheese muffins need to be refrigerated?

Yes. Because of the cream cheese filling, refrigerate leftovers after they have cooled, and eat within 5 days.

Can I use canned pumpkin for pumpkin muffins?

Yes, canned 100% pumpkin puree works perfectly. Avoid pumpkin pie filling, which has added sugar and spices.

Why did my cream cheese filling sink?

The batter may have been too thin or the filling too loose. Use softened, not melted, cream cheese and cover it with a thick layer of batter.

Can I make pumpkin cream cheese muffins ahead of time?

Yes. Bake them up to 2 days ahead and refrigerate, or freeze them for up to 3 months.