You’ll love this easy pumpkin cream cheese swirl muffin recipe. It's a delicious combination of my moist pumpkin muffin recipe topped with tangy sweet cream cheese. They take less than an hour to make and bake and show you how to make this tasty fall treat using simple ingredients.

These pumpkin muffins are one of my favorite fall treats. I love the combination of a moist sweet pumpkin muffin topped with tangy cream cheese and that little kick you get from the ginger in the homemade pumpkin pie spice.
If you’re in the mood for more pumpkin recipes, my pumpkin chocolate chip muffins and pumpkin streusel muffins are soft, moist, and full of fall spices. And if cream cheese is your thing, don’t miss my pumpkin bread with cream cheese frosting.
What Makes These Pumpkin Muffins So Good
I wanted to create an easy fall muffin recipe that brings together all my favorite flavors of the season: pumpkin, warm pumpkin spice, and a swirl of tangy cream cheese. These pumpkin cream cheese swirl muffins are soft, flavorful, and perfect for breakfast or an afternoon treat.
- The muffin method. I use the muffin method for this recipe because it’s quick and simple, and it produces moist, tender muffins every time. Mixing the wet and dry ingredients separately keeps the batter light and prevents over-mixing, which can make muffins dense.
- Baking at high temperature. To help the muffins rise tall with those bakery-style domes, I start baking them at 425°F, then lower the oven to 350°F. That initial burst of heat gives them a quick lift and a beautiful golden top.
Pumpkin Cream Cheese Swirl Muffin Ingredients
Here are the ingredients you need for these delicious pumpkin muffins:

- Pumpkin Puree: Libby’s Pumpkin Puree works best for these muffins. Be sure to use pumpkin puree and not pumpkin pie filling.
- Pumpkin Pie Spice: This recipe for homemade pumpkin pie spice is a delicious combination of ground cinnamon, ground ginger, ground nutmeg, and ground cloves. This spice mixture gives these muffins their distinctive warm flavor when combined with the pumpkin puree.
- Sour Cream: I love sour cream in my baked goods and it helps make these muffins moist and tender. Make sure to use full-fat sour cream instead of reduced fat or light.
- Cream Cheese: I recommend Philadelphia Brand Cream Cheese. It has the right amount of richness and tartness. Do not use whipped or light cream cheese.
Full ingredients, measurements, and instructions are in the recipe card at the bottom of this post.
How to Make Pumpkin Cream Cheese Swirl Muffins
Step 1: Melt the butter over medium-low heat. When there is just a small piece of butter left remove the pan from the heat and allow the butter to cool until it is just barely warm, about 80-85°F.
Melting the butter over low heat and removing it before it is completely melted will reduce the amount of evaporation. Most butter in the United States is 80% fat, 16% water, and about 2-4% milk solids, so we want to keep as much moisture as possible when melting the butter.
Step 2: Place the flour, baking soda, and baking powder in a medium bowl and whisk together to combine. Set the flour mixture aside.

Step 3: Place the brown sugar, granulated sugar, pumpkin pie spice, and salt in a large bowl and whisk together.

Step 4: Next add the warm butter and whisk it into the sugar mixture. It’s going to have a sandy texture.

Step 5: Whisk in the beaten eggs until the eggs are incorporated and the batter has a lighter color.

Step 6: Whisk in all of the pumpkin puree and whisk in the sour cream.

Step 7: Make the cream cheese swirl. Mix together the cream cheese, egg yolk, and sugar until thoroughly combined then mix in the vanilla extract.

Step 8: Add the dry ingredients in two batches, gently folding it in with a silicone spatula.

The batter will be stiff and a little lumpy, which is okay. Don’t overmix the batter trying to remove the lumps or the muffins will have a slightly rubbery texture.

Step 9: Divide the pumpkin muffin batter between the 12 muffin cups (about 80 grams in each muffin liner).

Step 10: Pipe six small dots of cream cheese around the top of the pumpkin batter. Use a toothpick or skewer to swirl the cream cheese around the top of each muffin.
Step 11: Bake the muffins until they have risen and the internal temperature registers 202°F. Check the internal temperature with an instant-read thermometer.

Remove the muffins from the oven, cool them for 5 minutes, and then place the muffins on a wire rack to finish cooling.

Pro Tips For Making These Muffins
- Use a scale to measure the flour to ensure you have the right amount. Too much flour could result in a dry muffin.
- Let the wet ingredients sit for 10 minutes to dissolve the sugar. Sugar contributes to the moisture of the muffins. Allowing the sugar to dissolve will help ensure a super moist muffin.
- Use room-temperature eggs and sour cream to help ensure a fluffy muffin. Cold eggs could result in stodgy muffins.
- Since this recipe does not use a whole can of pumpkin puree, store the leftover puree in an airtight container in the refrigerator for up to a week or freeze it until you're ready to use it for another recipe.

Did you make these pumpkin cream cheese muffins? If so, please leave a rating and a comment below. This helps my blog to grow.
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Moist and Tender Pumpkin Cream Cheese Swirl Muffins
Ingredients
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 (113 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) full-fat cream cheese room temperature
- 2 tablespoons (25 grams) granulated sugar
- 1 large (20 grams) egg yolk
- 1/2 teaspoon pure vanilla extract
Instructions
- 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.
Make the Muffin Batter
- 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 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
- 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.
How to Store the Muffins
- 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 toppin.
- I don’t recommend freezing the muffins. The cream cheese topping can be crumbly after thawing out and not taste as soon.





Sophie Ortiz says
Don't see the cinnamon, Nutmeg, ginger, on the list of ingredients
Cheryl Norris says
Hi Sophie
The cinnamon, nutmeg, and other spices are in the homemade pumpkin pie spice. I provided links in the blog post and recipe card for the pumpkin pie spice recipe.