Pumpkin Cream Cheese Swirl Muffins

Pumpkin Cream Cheese Swirl Muffins

These pumpkin muffins are one of my favorite treats. I love the combination of a moist sweet pumpkin muffin topped with tangy cream cheese. And it’s not only the cream cheese topping, but I love the taste of the spices and that little kick you get from the ginger in the homemade pumpkin pie spice.

You’ll love this recipe for Pumpkin Cream Cheese Swirl Muffins – it’s a delicious combination of moist pumpkin muffins topped with tangy sweet cream cheese and baked at hig. Plus they take less than an hour to make and bake. In the recipe below I’ll show you how to make this tasty treat using simple ingredients.

Two pumpkin cream cheese swirl muffins on a small plate with more muffins in the background

These moist fluffy muffins are full of warm fall spices – cinnamon, nutmeg, cloves, and ginger and topped with a tangy sweet cream cheese filling.

Prep Time: 25minutes 

Cook Time: 20minutes 

Total Time: 45minutes 

 Servings: 12 


Pumpkin Muffins

1-3/4 cups (220 grams) unbleached all-purpose flour

2 teaspoon (8 grams) baking powder

1/2 teaspoon baking soda

3/4 teaspoon kosher salt

8 tablespoons (114 grams) unsalted butter melted

1/2 cup (100 grams) packed dark brown sugar

1/2 cup (100 grams) granulated sugar

1 tablespoon pumpkin pie spice

2 large (100 grams) eggs room temperature (65-68 degrees F)

1 1/4 cups (280 grams) pumpkin puree Libby’s Pumpkin Puree, recommended

1/4 cup (60 grams) sour cream room temperature (65-68 degrees F)

Cream Cheese Filling

6 ounces (169 grams) cream cheese room temperature

2 tablespoons (25 grams) granulated sugar

1 large (20 grams) egg yolk

1/2 teaspoon pure vanilla extract


Pumpkin pie spice is one of the main ingredients in these muffins. Use this recipe for homemade pumpkin pie spice or purchase a jar from your local grocery store.

Preheat the oven to 425°F (220°C). Line a 12-cup muffin pan with paper liners.

Melt the butter in a small saucepan over low heat. When there is just a small piece of butter left, remove the saucepan from the heat. Beat the two eggs together in a small bowl.

Place the all-purpose flour, baking powder, baking soda, and salt in a medium sized bowl and whisk for 30 seconds to thoroughly combine the ingredients.
 Set the dry ingredients aside.

Place the brown sugar, granulated sugar, and pumpkin spice in a large bowl and whisk together. Use your fingers to break up any brown sugar clumps. Add the warm melted butter and whisk together until the ingredients are well combined, about 20 seconds. The mixture will have a sandy texture.

Add the beaten eggs and whisk until the eggs are thoroughly combined and the batter looks smoother and lighter in cooler. Whisk in the pumpkin puree, then whisk in the sour cream.

NOTE: If you’re using leftover pumpkin puree that’s been in the refrigerator, bring it room temperature (65-68 degrees F) before adding it to the batter. Adding cold pumpkin puree will cause the batter to curdle and may cause some of the butter to resolidify.

The batter should be lighter in color and look smooth. Set the batter aside for 10 minutes. Letting the batter sit for 10 minutes will give the sugar more time to thoroughly dissolve.

While the batter is sitting make the cream cheese filling. Place the cream cheese, sugar, and egg yolk in a small mixing bowl. Beat the ingredients together with a wooden spoon, until the ingredients are well combined. The batter may still be a little lumpy but that is okay. Mix in the vanilla extract.

Place the cream cheese mixture in a piping bag with a No. 12 Wilton tip. If you don’t have a piping bag, place the cream cheese in a freezer bag and cut a 1/4-inch opening into one of the bottom corners.

Add half of the flour mixture to the wet ingredients. Use a silicone spatula to fold the dry ingredients into the wet ingredients. Add the remaining flour mixture and fold it in until the dry ingredients are thoroughly incorporated, and no white specs of flour remain. Make sure to scrape from the bottom to ensure all the flour is incorporated into the batter.

The batter may be a little lumpy which is okay. Don’t try to make the batter smooth. That will cause the batter to be overmixed which will result in tough springy muffins.

Divide the batter between the 12 muffin cups. The batter should almost be the top of each paper liner. If you’re using a kitchen scale, that’s about 80 grams of batter for each muffin cup.

Next pipe 6 drops of the cream cheese around the top of each muffin with at least one in the center. It should come to about 1 tablespoon of cream cheese per muffin. Use a toothpick or wooden skewer to swirl the cream cheese across the top.

Bake the muffins at 425°F for 5 minutes, then without opening the oven door reduce the temperature to 350°F (180°C). Bake the muffins for another 15-18 minutes, until the center is done.

Test for doneness by sticking a toothpick or a cake skewer in the center. There should be no more than 1 or 2 crumbs sticking to the toothpick. For a temperature, the temperature in the center of the muffin should register 202 degrees F using an instant-read thermometer.

Remove the muffins from the oven and let the muffins cool in the muffin pan for 5 minutes. Place the individual muffins on a wire rack to finish cooling. The muffins can be served warm.


Place the muffins in an airtight container in the refrigerator the same day they are baked and after you’ve finished eating them for the day. The muffins need to be refrigerated because of the cream cheese topping.

I don’t recommend freezing the muffins. The cream cheese topping can be crumbly after thawing out and not taste as soon.


Pumpkin Pie Spice: Use this recipe for pumpkin pie spice to make your own. It will keep up to 2 years depending on the age of your spices when you make it.

Weigh the Ingredients: The best and most consistent results will come my weighing the flour, butter, sour cream, and pumpkin puree. Not only do you get the best results, but there are also fewer dirty dishes because you’re measuring directly into the mixing bowls.

Leftover Pumpkin Puree: This recipe doesn’t use a full can of pumpkin puree. Store leftover puree in an airtight container for up to 7 days. Or freeze it for up to a few months, based on the expiration date on the can.


Calories: 238kcal | Carbohydrates: 25g | Protein: 3g | Fat: 15g | Saturated Fat: 9g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Trans Fat: 0.3g | Cholesterol: 84mg | Sodium: 325mg | Potassium: 111mg | Fiber: 1g | Sugar: 21g | Vitamin A: 4492IU | Vitamin C: 1mg | Calcium: 85mg | Iron: 1mg

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