Cream Cheese-Stuffed Pumpkin Muffins for Fall Baking

If you’re searching for a truly satisfying muffin, these pumpkin cream cheese muffins are a perfect choice. Spiced pumpkin muffins with a soft cream cheese center, finished with a sprinkle of sunflower seeds—simple, delicious, and ideal any time of day.

Pumpkin Cream Cheese Muffins sitting on parchment paper with a cup of coffee.

Tired of the same old muffin? These combine classic pumpkin spice flavors with a creamy, lightly sweetened center for a delightful contrast of textures and tastes.

They’re easy to make and full of fall flavor. Serve them warm with coffee for breakfast, pack them for a snack, or enjoy one as a little dessert.

I topped mine with sunflower seeds for a nutty crunch, but shelled pumpkin seeds work just as well if you prefer.

Moist, tender, and straightforward to prepare—these muffins will quickly become a favorite.

Pumpkin Cream Cheese Muffins cut in half.

What do I need to make pumpkin cream cheese muffins?

This recipe uses common pantry ingredients, though a few items like cream cheese and pumpkin puree are essential for the signature flavor and texture.

  • Cream cheese – softened to room temperature for a smooth filling.
  • Egg white – helps bind the cream cheese mixture.
  • Powdered sugar – sweetens the cream cheese filling.
  • Vanilla extract – enhances flavor; vanilla paste can be used instead.
  • Pumpkin puree – canned gives consistent results, but homemade is fine.
  • Eggs – bind the pumpkin batter.
  • Vegetable oil – keeps the muffins moist.
  • Milk – 2% or whole milk works well; nondairy milk is fine too.
  • All-purpose flour – unbleached is preferred; whole white wheat can be substituted.
  • Brown sugar – light or dark brown sugar both work.
  • Baking powder and baking soda – give the muffins lift.
  • Kosher salt – balances the sweetness.
  • Cinnamon, nutmeg, ginger, allspice – warm fall spices that define the flavor.
  • Sunflower seeds – for topping; shelled pumpkin seeds are a good alternative.
Pumpkin Cream Cheese Muffins sitting on a board with coffee.

What is the best canned pumpkin?

Brands like Libby’s and Trader Joe’s are reliable and widely available. Great Value (Walmart) also works well. The main goal is consistency—choose a brand that delivers the same texture and flavor each time.

Can I use different spices?

Absolutely. If you don’t have each individual spice, substitute 1 tablespoon of pumpkin pie spice for the combined cinnamon, nutmeg, ginger, and allspice measurements.

Pumpkin Cream Cheese Muffins broken in half.

How do I store leftover muffins?

Store muffins covered at room temperature for up to three days. If your environment is warm or humid, refrigerate them after 24 hours to preserve freshness.

Pumpkin Cream Cheese Muffins served with a cup of coffee.

Can I freeze pumpkin cream cheese muffins?

Yes. Place cooled muffins in freezer-safe containers or bags and store for up to three months. Thaw at room temperature or in the fridge before serving.

Pumpkin Cream Cheese Muffins stacked on a white board.

Love these pumpkin cream cheese muffins?

If you enjoy these, try other pumpkin-forward recipes for more seasonal inspiration.

  • Pumpkin Yeast Bread
  • Spicy Thai Pumpkin Soup
  • Butterscotch Pumpkin Bundt Cake
  • Pumpkin Spice Whipped Coffee
  • Pumpkin Churro Cheesecake Bars

5 from 4 votes

Pumpkin Cream Cheese Muffins

By: Brandy O’Neill
Servings: 12 muffins
Prep: 15
Cook: 25
Total: 40
img 18599 7
If you’re looking for the perfect muffin look no further than these pumpkin cream cheese muffins. Spiced pumpkin muffins topped with cream cheese and topped with sunflower seeds. You’ll love these easy and simple pumpkin muffins!

Ingredients 

For cream cheese mixture:

  • 8 ounces cream cheese, room temperature
  • 1 large egg white
  • 1/4 cup powdered sugar
  • 1/2 teaspoon vanilla extract

For pumpkin batter:

  • 3/4 cup pumpkin puree
  • 2 large eggs
  • 1/3 cup vegetable oil
  • 1/3 cup milk
  • 1-1/2 teaspoons vanilla extract
  • 1-1/2 cup all-purpose flour
  • 3/4 cup light brown sugar, lightly packed
  • 1-1/2 teaspoons cinnamon
  • 1-1/4 teaspoons baking powder
  • 1/2 teaspoon nutmeg
  • 1/4 teaspoon baking soda
  • 1/4 teaspoon kosher salt
  • 1/4 teaspoon ginger
  • 1/4 teaspoon allspice
  • 4 teaspoons raw, shelled sunflower seeds

Instructions 

  • Preheat oven to 350°F and line a 12-cup muffin tin with paper liners.
  • Make the cream cheese filling: beat cream cheese, egg white, powdered sugar, and 1/2 teaspoon vanilla until smooth. Set aside.
  • In another bowl, whisk pumpkin puree, eggs, oil, milk, and 1-1/2 teaspoons vanilla until combined.
  • In a large bowl, whisk together flour, brown sugar, cinnamon, baking powder, nutmeg, baking soda, kosher salt, ginger, and allspice.
  • Add the pumpkin mixture to the dry ingredients and stir until just combined—do not overmix.
  • Fill each muffin cup about two-thirds full with pumpkin batter, reserving roughly 6 tablespoons for topping.
  • Spoon the cream cheese mixture over each muffin, then add about 1/2 tablespoon of the reserved pumpkin batter on top. Sprinkle with sunflower seeds.
  • Bake 20–25 minutes, until a toothpick inserted into the muffin (not the cream cheese center) comes out clean or with a few crumbs.
  • Cool completely before storing. Keep covered at room temperature up to 3 days, or refrigerate if needed.

Additional Info

Course: Muffins
Cuisine: American
Pumpkin Cream Cheese Muffins pin for pinterest.