Pumpkin Cream Cheese Muffins

The combination of pumpkin spice and tangy cream cheese swirled together in this Pumpkin Cream Cheese Muffins means breakfast just got a whole lot better.

Pumpkin muffins stacked on a plate with a white pumpkin behind it.

Cambrea Gordon

Pumpkin muffins are a classic for fall baking season and they’re a classic for a reason. The muffins are full of sweet pumpkin flavor, warm baking spices, and even their color is deeply autumnal. This recipe takes a classic muffin and makes them extra special with cream cheese swirl.

The combination of pumpkin spice and tangy cream cheese brings the extra comfort you need to welcome the colder weather. They’re almost like pumpkin cheesecake, except you can have them for breakfast.

These Pumpkin Cream Cheese Muffins are an easy and indulgent treat for a cold fall morning. They’re a welcoming recipe to share with friends and family, or you could even just make a batch for yourself. They would be an especially festive way to kick off a Thanksgiving breakfast or brunch.

What You Need to Make Pumpkin Cream Cheese Muffins

It’s not just the cream cheese swirl that makes these muffins so exceptional. This recipe was designed to look enticing enough to be the brunch centerpiece without all the work of a centerpiece.

They don’t require any special equipment, they’re ready to serve in an hour, and they taste amazing. By maximizing what you get from each ingredient, this recipe does the work for you.

Pumpkin purée: This muffin recipe uses an entire 15 ounce can of pumpkin purée, so they’re incredibly moist and loaded with pumpkin flavor. Plus, you don’t have to figure out what to do with an odd amount of leftover pumpkin purée. Be sure to use 100 percent pure pumpkin and not canned pumpkin pie filling.

Pumpkin pie spice: These muffins pack a punch with a tablespoon of pumpkin pie spice. They feature all the favorite fall spices, like cinnamon, ginger, nutmeg, cloves, and allspice. You can use a store-bought spice mix or make your own blend and keep it in a jar in your spice cabinet for up to 6 months for all your upcoming pumpkin bakes.

Light brown sugar: The subtle molasses flavor of light brown sugar complements the pumpkin and spices without overwhelming them, so it’s the only type of sugar used in this recipe. Brown sugar also retains moisture well, making these muffins extra soft and tender.

Cream cheese: What better way to level up pumpkin muffins than by adding creamy, tangy cream cheese. The richness of cream cheese along with pumpkin spice creates a creamy, light balance between texture and flavor. They look nice too!

Pumpkin swirl cut in half to show the swirls.

Cambrea Gordon

Tips for Making the Best Pumpkin Muffins

While a cream cheese swirl and some streusel can hide any mishaps along the way, there are a few tips that can help you make the best pumpkin muffins every time.

  • Make the cream cheese mixture before you make the muffin batter. Muffins and quick breads should be baked immediately after being mixed. By having the cream cheese mixture ready for swirling, the muffin batter won’t sit very long before baking.
  • Try not to overmix the muffin batter. If the batter is overmixed the muffins won’t rise as much, they will be tough, and there will be large uneven holes throughout. The batter doesn’t need to be mixed until smooth, just until it’s moistened and there are no streaks of dry flour. It is okay if the batter is a little lumpy.
  • To divide the batter neatly and evenly among the muffin cups, it’s helpful to use a cookie scoop or an ice cream scoop with a trigger. Or, if you don’t have one, use a liquid measuring cup with a spout to pour the batter into the cups mess-free.
  • The pan will be very full. You will fill the muffin wells nearly to the top. This results in their tall, bakery-style look.
  • Let them cool for at least 5 minutes before removing them from the pan, then allow them to cool for at least another 10 minutes before serving. This gives them time to set properly as they may be too delicate when still warm.

How to Make the Cream Cheese Swirl

The best cream cheese for this filling is the full-fat cream cheese that comes in a block. The cream cheese in a tub is formulated with a higher moisture content to spread easier.

TIP: If you only have cream cheese in a plastic tub, add a tablespoon of flour to the filling. The flour will absorb some of the extra moisture for a smooth cheesecake texture.

Divide the pumpkin muffin batter evenly between each muffin tin. Top the muffin batter with about a tablespoon of the cream cheese filling. Then, stir the cream cheese and pumpkin muffin batter together into a swirly pattern. I like to use a butter knife, but you can use a toothpick, a small offset spatula, or a chopstick.

Fall pumpkin muffins on a plate with butter on the side.

Cambrea Gordon

How to Store Pumpkin Cheesecake Muffins

The muffins will keep in an airtight container on the counter for up to 2 days, or in the refrigerator for up to a week. Let them come to room temperature or warm them before serving if you are storing in the fridge.

Cream cheese, unfortunately, doesn’t freeze very well, so they’re best enjoyed fresh.

More Great Pumpkin Recipes

Pumpkin Cream Cheese Muffins

Prep Time 30 mins
Cook Time 20 mins
Total Time 50 mins
Servings 12 servings

This muffin batter is thick. If using a muffin tin liner its best to use a sturdy one such as silicone or aluminum. It will stay better than paper liners when swirling in the cream cheese.

Special equipment: standard muffin pan, silicon or aluminum muffin liners


For the pumpkin spice streusel

  • 3/4 cup (90g) all-purpose flour

  • 1/4 cup (54g) light brown sugar, packed

  • 2 teaspoons pumpkin pie spice

  • 1/4 cup (57g) unsalted butter, melted

For the cream cheese filling

  • 6 ounces cream cheese, at room temperature

  • 1 large egg yolk

  • 1/4 cup (50g) granulated sugar

  • 1/2 teaspoon vanilla extract

For the pumpkin muffins

  • 2 cups (240g) all-purpose flour

  • 1 tablespoon pumpkin pie spice

  • 1 1/2 teaspoons baking powder

  • 1/2 teaspoon baking soda

  • 1/2 teaspoon salt

  • 1 (15 ounce) can pumpkin puree

  • 1 1/4 cups (270g) light brown sugar, packed

  • 2 large eggs

  • 1/2 cup vegetable oil


  1. Preheat oven and prepare the muffin tin:

    Preheat the oven to 375°F. Line a standard muffin pan with muffin liners, or if you don’t have muffin liners, grease each well with butter and dust with flour, tapping out the excess.

  2. Make the pumpkin pie spice streusel:

    In a small bowl, whisk together the flour, brown sugar, and pumpkin pie spice. Pour in the melted butter and mix with a fork until crumbs form. Set aside until ready to use.

    Making the streusel for pumpkin muffins

    Cambrea Gordon

  3. Make the cream cheese filling:

    In a medium mixing bowl, whisk together the cream cheese, egg yolk, sugar, and vanilla extract until smooth and creamy, similar in thickness to vanilla custard.

    Mixing the cream cheese filling for pumpkin cream cheese swirl muffins

    Cambrea Gordon

  4. Mix the dry ingredients:

    In a large mixing bowl, whisk together the flour, pumpkin pie spice, baking powder, baking soda, and salt.

    Mixing the dry ingredients to make pumpkin muffins.

    Cambrea Gordon

  5. Mix the wet ingredients:

    In a mixing bowl, add the pumpkin purée, brown sugar, eggs, and vegetable oil. Whisk until combined.

    Mixing the batter for fall pumpkin muffins.

    Cambrea Gordon

  6. Make the batter:

    Pour the pumpkin mixture into the flour mixture. Stir with a large spoon or a rubber spatula just until combined and no streaks of flour remain. Do not overmix. It is okay if there are some lumps in the batter.

  7. Divide the muffin batter:

    Divide the batter evenly among the muffin tin. Each well should be filled nearly to the top, though you do need room to swirl in 1 tablespoon of cream cheese filling.

    Fall pumpkin muffin batter in a muffin tin.

    Cambrea Gordon

  8. Swirl in the cream cheese filling:

    Spoon a tablespoon of the cream cheese filling on the top of each muffin and use a butter knife to loosely stir it into the batter to make a swirl pattern. Swirl in the cream cheese in a figure 8 pattern while pulling some of the batter up from the bottom.

    Swirling in cream cheese into pumpkin muffins.

    Cambrea Gordon

  9. Add the pumpkin pie spice streusel:

    Sprinkle the streusel over each of the muffins.

    Streusel topped muffins ready for the oven.

    Cambrea Gordon

  10. Bake the muffins:

    Place the muffins in the oven and bake for about 20 minutes, or until a toothpick inserted in the center comes out clean.

    Testing doneness of pumpkin cream cheese swirl muffins with a toothpick.

    Cambrea Gordon

  11. Cool muffins and serve:

    Allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack to cool for at least 10 minutes more. Serve.

    Pumpkin cream cheese muffins with pumpkin spice streusel cooling on a rack.

    Cambrea Gordon

Nutrition Facts (per serving)
421 Calories
20g Fat
56g Carbs
6g Protein
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Nutrition Facts
Servings: 12
Amount per serving
Calories 421
% Daily Value*
Total Fat 20g 25%
Saturated Fat 7g 33%
Cholesterol 86mg 29%
Sodium 275mg 12%
Total Carbohydrate 56g 20%
Dietary Fiber 2g 7%
Total Sugars 32g
Protein 6g
Vitamin C 2mg 8%
Calcium 98mg 8%
Iron 2mg 14%
Potassium 182mg 4%
*The % Daily Value (DV) tells you how much a nutrient in a food serving contributes to a daily diet. 2,000 calories a day is used for general nutrition advice.
Nutrition information is calculated using an ingredient database and should be considered an estimate. In cases where multiple ingredient alternatives are given, the first listed is calculated for nutrition. Garnishes and optional ingredients are not included.