Pumpkin Cream Cheese Muffins Recipe for a Cozy Fall Morning

Pumpkin Cream Cheese Muffins

If pumpkin bread and cheesecake had a muffin baby, this is what it would taste like. These homemade pumpkin cream cheese muffins bake at 350ºF into moist, warmly spiced cakes with a tangy cream cheese center that makes a coffee shop run feel completely unnecessary.

The recipe makes 16 muffins with 15 minutes of prep and about 20 minutes in the oven, so 35 minutes from mixing bowl to cooling rack. You also get two ways to build them: a decorative swirl or a thick, cheesecake style center.

When Pumpkin Meets Cheesecake

I have been baking pumpkin muffins every October for longer than I care to admit, and this is the version that finally stopped me from buying them at the drive through.

The pumpkin batter is soft, deeply spiced, and just sweet enough, and the cream cheese filling cuts through all of that warmth with a cool, tangy richness. Pumpkin and cheesecake are a natural pair.

One is earthy and caramel sweet, the other is bright and creamy, and together they taste like the best part of a bakery case.

The reason I keep coming back to this particular formula is the testing behind it. The author has remade these muffins for years, trying two very different ways of getting the cream cheese into the batter, and both of them work.

In one version the filling is piped into the middle of each muffin, which gives you a thick cheesecake style core that stays put through baking.

In the other, scoops of pumpkin batter and cream cheese are layered and swirled together, which creates marbled ribbons and a prettier top.

Both options land in the same place: a moist muffin with a creamy center and a domed, lightly crisp top. If you are feeding a crowd at a fall potluck, the swirl is the showpiece.

If you want that unmistakable coffee shop bite where the filling sits in one generous pocket, go with the piped version. Either way, the muffins stay tender for days, which is not something I can say about most quick breads.

Ingredients You’ll Need

Before you measure anything, a few ingredient notes are worth reading. They are the difference between a muffin that tastes straight out of the bakery case and one that turns out dense or bland.

• Canned pumpkin: Use 1 cup of 100% pure pumpkin purée, not pumpkin pie filling. Pie filling is already sweetened and spiced, so it throws off the balance. You will have some pumpkin left in the can, so freeze the extra in small portions or stir it into pancakes and oatmeal. If you make your own purée, drain off the excess liquid first, otherwise the muffins bake up heavy.
• Cream cheese: One 8 ounce package of full fat block cream cheese, at room temperature. The spreadable tub kind carries more water and will not set into that thick cheesecake center.
• Pumpkin pie spice: 2 1/2 teaspoons. Store bought works beautifully, and a homemade blend of cinnamon, ginger, nutmeg, and cloves is lovely if you already keep one in the cupboard.
• Unsalted butter: 1/2 cup at room temperature. Butter gives a richer flavor and a slightly denser crumb than oil based muffins, and room temperature butter creams smoothly with the sugar so the batter stays even.
• Vanilla extract: It goes into both the batter and the filling, so the two layers taste like they belong together.

Here is the full list, grouped so you can work through it quickly.

For the muffins

• 1 2/3 cups all purpose flour
• 1/2 teaspoon baking powder
• 1 teaspoon baking soda
• 1/2 teaspoon salt
• 2 1/2 teaspoons pumpkin pie spice
• 1/2 cup unsalted butter, at room temperature
• 1 1/3 cups sugar
• 1/2 teaspoon vanilla extract
• 2 large eggs
• 1 cup canned pumpkin
• 1/3 cup water

For the cream cheese filling

• 1 (8 ounce) package cream cheese, at room temperature
• 2 Tablespoons sugar
• 1 large egg
• 1 teaspoon vanilla extract

Kelly’s Note from the Test Kitchen

This recipe was first shared back in 2015, and it has been made dozens of times since, which is exactly why I trust it. Sometimes the cream cheese mixture gets piped into the center of each muffin.

Sometimes scoops of pumpkin batter and cheesecake filling are alternated in the cups and swirled with a toothpick. Both techniques have been tested repeatedly, and both turn out delicious. There is no wrong answer here, only two different looks. Pick the one that matches the mood of your morning.

How to Make Pumpkin Cream Cheese Muffins (Two Ways!)

The batters are forgiving, so either approach produces a great muffin. Start by preheating the oven to 350ºF and lining a muffin pan with baking cups.

1. In a large bowl, sift together the flour, baking powder, baking soda, salt, and pumpkin pie spice. Set it aside.
2. In the bowl of a stand mixer fitted with the paddle attachment, cream the butter, sugar, and vanilla until light and fluffy, about 2 minutes. Add the eggs one at a time, then the pumpkin, and mix until combined.
3. Alternately add the dry ingredients and the water, beginning and ending with the dry ingredients. Blend well, scraping down the sides as needed, then set the batter aside.
4. In the same mixer bowl, beat the cream cheese, sugar, egg, and vanilla until smooth.

Option 1: Cream Cheese Filled Muffins

Spoon the pumpkin batter into the prepared cups, filling each about three quarters full. Chill the cream cheese mixture for 10 to 15 minutes. Chilling firms it up so it pipes neatly and holds its shape instead of spreading into the batter.

Transfer the filling to a piping bag, or to a resealable plastic bag with one corner snipped off, and pipe about 1 1/2 tablespoons into the center of each cup. The tip should sit just below the surface of the batter.

Do not overfill, and do not push the filling all the way to the bottom, or it will sink and pool during baking.

Option 2: Swirled Pumpkin Cheesecake Muffins

For the marbled look, alternate dollops of pumpkin batter and cream cheese filling in each cup until they are about three quarters full. Then drag a toothpick or a thin skewer through the mixture in two or three gentle figure eight motions.

Less is more here. Overworking the swirl blends the two batters into a muddy beige and you lose those distinct cheesecake ribbons. Stop while you can still see both colors.

Bake & Cool

Bake at 350ºF for 20 to 25 minutes, until the tops feel lightly springy and a toothpick inserted into the muffin just beside the cream cheese center comes out mostly clean with a few moist crumbs. Test beside the filling rather than through it.

A toothpick that hits the cheesecake center will come out wet no matter how done the muffin is, and you will end up overbaking the whole batch chasing a clean tester.

Let the muffins cool in the pan for about 5 minutes, then move them to a wire rack to cool completely. This part matters more than it sounds. As they cool, the pumpkin flavor deepens and the cheesecake centers firm up, so a muffin that tastes a little soft at 10 minutes tastes exactly right at 30.

Success Tips & Variations

These are the small habits that separate a good muffin from a great one.

• Bring everything to room temperature. Butter, eggs, and cream cheese should all sit out for about an hour before you start. Room temperature ingredients blend into a smooth batter and a silky filling, with no lumps of cold cream cheese hiding in the middle.
• Use muffin liners. Paper liners keep the muffins from sticking, encourage even rising, and make cleanup quick.
• Fill cups about three quarters full. Going higher causes spillover and flat, lopsided tops. A little restraint gives you tall, domed muffins every time.
• Try the mini bread version. The same batter and filling work in a mini pumpkin cream cheese bread, which slices beautifully and makes a lovely gift for neighbors and teachers.
• Add a crunchy finish. Sprinkle pumpkin seeds, also called pepitas, over the tops before baking. It adds a little salt and crunch and gives the muffins that coffee shop bakery look.

Storage and Freezing Tips

Because of the cream cheese filling, these muffins are a refrigerator recipe. Keep them in an airtight container in the fridge for up to 5 days. They are excellent straight from the cold, and they are excellent after 20 minutes on the counter, so serve them whichever way you prefer.

Freezing works too, with one honest caveat. The cheesecake centers can turn slightly softer or a little grainy after thawing. To minimize that, freeze the muffins as soon as they are completely cool.

Arrange them in a single layer on a baking sheet until firm, then move them to a freezer safe container or bag with parchment between the layers. They keep for up to 2 months.

Thaw them overnight in the fridge and warm them for a few minutes in a 300ºF oven if you want that fresh from the bakery feel.

One more freezer note: skip the paper liners if you plan to freeze. They tend to pull away from the muffin after thawing. Instead, grease the muffin tin generously with cooking spray and bake the muffins directly in the pan.

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Pumpkin Cream Cheese Muffins

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Pumpkin Cream Cheese Muffins If pumpkin bread and cheesecake had a muffin baby, this is what it would taste like. These homemade pumpkin cream cheese muffins bake at 350ºF into moist, warmly spiced cakes with a tangy cream cheese center that makes a coffee shop run feel completely unnecessary.

• Total Time: 35 min
• Yield: 16 muffins 1x

Ingredients

Scale 1x2x3x

For the muffins
1 2/3 cups all-purpose flour
1/2 teaspoon baking powder
1 teaspoon baking soda
1/2 teaspoon salt
2 1/2 teaspoons pumpkin pie spice
1/2 cup unsalted butter, at room temperature
1 1/3 cups sugar
1/2 teaspoon vanilla extract
2 large eggs
1 cup canned pumpkin
1/3 cup water

For the cream cheese filling
1 (8-oz.) package cream cheese, at room temperature
2 Tablespoons sugar
1 large egg
1 teaspoon vanilla extract

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Instructions

Make the muffins
1-Preheat the oven to 350ºF: Preheat the oven to 350ºF. Line a muffin pan with baking cups.
2-In a large bowl, sift together the: In a large bowl, sift together the flour, baking powder, baking soda, salt and pumpkin pie spice. Set the bowl aside.
3-In the bowl of a stand mixer: In the bowl of a stand mixer fitted with the paddle attachment, cream together the butter, sugar and vanilla until light and fluffy, about 2 minutes. Add the eggs, one at a time, then add the pumpkin and mix until combined.
4-Alternately add the dry ingredients and water: Alternately add the dry ingredients and water to the bowl, beginning and ending with the dry ingredients. Blend the batter well, scraping down the sides as needed. Set the batter aside.

Make the cream cheese filling
5-In the bowl of a stand mixer: In the bowl of a stand mixer fitted with the paddle attachment, beat together the cream cheese, sugar, egg and vanilla.
6-Alternately add dollops of the pumpkin batter: Alternately add dollops of the pumpkin batter and cream cheese filling into the muffin cups, filling each ¾ full. Using a toothpick or sharp knife, swirl together the mixture.
7-Bake the muffins for 20 to 25: Bake the muffins for 20 to 25 minutes or until a toothpick inserted comes out clean. Allow the muffins to cool in the pan for 5 minutes then transfer them to a rack to cool completely.

Last Step:

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• Prep Time: 15 min
• Cook Time: 20 min
• Method: bake

Nutrition

• Calories: 188kcal
• Sugar: 18g
• Sodium: 155mg
• Fat: 6g
• Saturated Fat: 3g
• Carbohydrates: 29g
• Protein: 2g
• Cholesterol: 46mg