Pumpkin Cream Cheese Muffins

Name: Pumpkin Cream Cheese Muffins
Prep time: 20 min
Cook time: 20 min
Total time: 50 min
Yield: 12 muffins
Cuisine: International
Ingredients: 8 ounces full-fat cream cheese, softened to room temperature; 1/4 cup granulated sugar; 1 large egg yolk, at room temperature; 1/2 teaspoon vanilla extract; 1 small pinch fine salt; 1 3/4 cups all-purpose flour, spooned and leveled; 1 teaspoon baking soda; 1/2 teaspoon baking powder; 2 teaspoons pumpkin pie spice; 1/2 teaspoon ground cinnamon; 1/2 teaspoon fine salt; 1 cup canned pumpkin puree, not pumpkin pie filling; 1/2 cup packed light brown sugar; 1/2 cup granulated sugar; 1/2 cup neutral oil, such as canola, vegetable, or avocado oil; 2 large eggs, at room temperature; 1/4 cup whole milk, at room temperature; 1 teaspoon vanilla extract; 2 tablespoons pepitas, for a nutty crunch; Or 2 tablespoons coarse sparkling sugar, for a sweet bakery-style top

Imperial June 10, 2026June 10, 2026

Quick Recipe Version (TL;DR)

Yield: 12 muffins
Prep Time: 20 minutes
Cook Time: 20 minutes
Total Time: 50 minutes, including 10 minutes cooling in the pan

Quick Ingredients

Cream cheese filling: 8 ounces full-fat cream cheese, 1/4 cup granulated sugar, 1 large egg yolk, 1/2 teaspoon vanilla extract, pinch of fine salt
Dry ingredients: 1 3/4 cups all-purpose flour, 1 teaspoon baking soda, 1/2 teaspoon baking powder, 2 teaspoons pumpkin pie spice, 1/2 teaspoon ground cinnamon, 1/2 teaspoon fine salt
Wet ingredients: 1 cup pumpkin puree, 1/2 cup packed light brown sugar, 1/2 cup granulated sugar, 1/2 cup neutral oil, 2 large eggs, 1/4 cup whole milk, 1 teaspoon vanilla extract
Optional topping: 2 tablespoons pepitas or coarse sparkling sugar

Do This

1. Heat oven to 350°F and line a 12-cup muffin pan with paper liners.
2. Beat the cream cheese filling ingredients until smooth and set aside.
3. Whisk flour, baking soda, baking powder, spices, and salt in one bowl.
4. Whisk pumpkin, sugars, oil, eggs, milk, and vanilla in another bowl, then fold in the dry ingredients.
5. Fill each muffin cup with batter, add cream cheese filling in the center, top with more batter, and swirl a little filling on top.
6. Bake for 18 to 22 minutes, until the muffin portion springs back and a toothpick inserted into the cake part comes out with moist crumbs.
7. Cool in the pan for 10 minutes, then transfer to a rack and cool at least 20 minutes more so the filling sets.

Why You’ll Love This Recipe

Cozy and warmly spiced: Pumpkin puree, pumpkin pie spice, cinnamon, and brown sugar make these muffins taste like autumn in bakery form.
Creamy cheesecake-style center: The sweet cream cheese filling bakes into a soft, tangy surprise inside each muffin.
Moist but not heavy: Oil, pumpkin, eggs, and a small splash of milk create a tender crumb that stays soft for days.
Impressive but easy: The swirl looks special, but the method is simple enough for a relaxed weekend bake.

Grocery List

Produce: None required
Dairy: 8 ounces full-fat cream cheese, 2 large eggs plus 1 large egg yolk, whole milk
Pantry: All-purpose flour, canned pumpkin puree, granulated sugar, light brown sugar, neutral oil, baking soda, baking powder, pumpkin pie spice, ground cinnamon, fine salt, vanilla extract, optional pepitas or coarse sparkling sugar

Full Ingredients

For the Cream Cheese Filling

8 ounces full-fat cream cheese, softened to room temperature
1/4 cup granulated sugar
1 large egg yolk, at room temperature
1/2 teaspoon vanilla extract
1 small pinch fine salt

For the Pumpkin Muffin Batter

1 3/4 cups all-purpose flour, spooned and leveled
1 teaspoon baking soda
1/2 teaspoon baking powder
2 teaspoons pumpkin pie spice
1/2 teaspoon ground cinnamon
1/2 teaspoon fine salt
1 cup canned pumpkin puree, not pumpkin pie filling
1/2 cup packed light brown sugar
1/2 cup granulated sugar
1/2 cup neutral oil, such as canola, vegetable, or avocado oil
2 large eggs, at room temperature
1/4 cup whole milk, at room temperature
1 teaspoon vanilla extract

Optional Topping

2 tablespoons pepitas, for a nutty crunch
Or 2 tablespoons coarse sparkling sugar, for a sweet bakery-style top

Step-by-Step Instructions

Step 1: Prepare the oven and muffin pan

Preheat the oven to 350°F. Line a standard 12-cup muffin pan with paper liners. If you are not using liners, grease the muffin cups well with nonstick spray, paying attention to the top edges of the pan where the muffins may rise slightly.

Step 2: Make the cream cheese filling

In a medium bowl, beat the softened cream cheese with the granulated sugar, egg yolk, vanilla extract, and a small pinch of salt until completely smooth and creamy. You can use a hand mixer on medium speed for about 1 minute, or mix firmly with a spatula if the cream cheese is very soft.

The filling should look thick, glossy, and spreadable, with no large lumps of cream cheese. Set it aside while you prepare the muffin batter.

Step 3: Mix the dry ingredients

In a large bowl, whisk together the all-purpose flour, baking soda, baking powder, pumpkin pie spice, cinnamon, and fine salt for about 20 seconds. This evenly distributes the leavening and spices so every muffin rises well and tastes warmly spiced throughout.

Step 4: Mix the pumpkin batter

In a separate large bowl, whisk together the pumpkin puree, light brown sugar, granulated sugar, neutral oil, eggs, whole milk, and vanilla extract until smooth and well combined. The mixture should be glossy and deep orange.

Add the dry ingredients to the wet ingredients. Using a spatula, gently fold just until you no longer see dry streaks of flour. Do not overmix; a few tiny lumps are fine. Overmixing can make muffins tough instead of soft and tender.

Step 5: Fill the muffin cups

Spoon about 2 tablespoons of pumpkin batter into each lined muffin cup. Add about 1 level tablespoon of cream cheese filling to the center of each muffin, keeping it slightly away from the edges if possible.

Top each muffin with the remaining pumpkin batter, about 1 to 1 1/2 tablespoons per cup. The cups should be about three-quarters full. If you have a little cream cheese filling left, add a small dollop to the top of each muffin.

Step 6: Swirl the tops

Use a toothpick, skewer, or the tip of a small knife to gently swirl the top dollop of cream cheese into the pumpkin batter. Make only 2 to 3 small figure-eight motions per muffin. Avoid over-swirling, which can blend the filling into the batter instead of leaving a pretty cream cheese ribbon.

If using pepitas or coarse sparkling sugar, sprinkle a small pinch over the tops before baking.

Step 7: Bake the muffins

Bake at 350°F for 18 to 22 minutes, or until the pumpkin muffin portion springs back lightly when touched. A toothpick inserted into the cake portion, not directly through the cream cheese center, should come out with a few moist crumbs but no wet batter.

The cream cheese swirl may still look slightly soft when the muffins come out of the oven. That is normal; it will set more as the muffins cool.

Step 8: Cool and serve

Let the muffins cool in the pan for 10 minutes. Carefully transfer them to a wire rack and let them cool for at least 20 minutes more before serving. This short cooling time helps the cheesecake-like filling settle so each muffin has a creamy center rather than a runny one.

Serve slightly warm, at room temperature, or chilled. The flavor becomes even richer after the muffins have rested for a few hours.

Pro Tips

Use pumpkin puree, not pumpkin pie filling: Pumpkin pie filling already contains sugar and spices, which would make the muffins too sweet and throw off the texture.
Soften the cream cheese fully: Room-temperature cream cheese blends smoothly and gives you a prettier swirl without lumps.
Do not overmix the batter: Fold gently and stop as soon as the flour disappears. This keeps the muffins soft and bakery-tender.
Check the cake portion for doneness: If your toothpick hits the cream cheese center, it may look wet even when the muffin is fully baked.
Cool before digging in: The muffins are delicious warm, but the cream cheese filling needs at least 20 minutes on a rack to firm up properly.

Variations

Streusel-topped pumpkin cream cheese muffins: Mix 1/4 cup flour, 2 tablespoons brown sugar, 1/4 teaspoon cinnamon, and 2 tablespoons cold butter until crumbly. Sprinkle over the muffins before baking.
Chocolate chip version: Fold 1/2 cup mini chocolate chips into the pumpkin batter before filling the muffin cups.
Maple spice version: Replace 2 tablespoons of the granulated sugar in the batter with 2 tablespoons pure maple syrup and add 1/8 teaspoon ground cloves for a deeper fall flavor.

Storage & Make-Ahead

Because these muffins contain a cream cheese filling, store them in an airtight container in the refrigerator for up to 5 days. Let them sit at room temperature for 15 to 20 minutes before serving, or warm one muffin in the microwave for 10 to 12 seconds if you prefer a softer texture.

To freeze, place completely cooled muffins on a baking sheet and freeze until firm, about 1 hour. Transfer to a freezer-safe bag or container and freeze for up to 2 months. Thaw overnight in the refrigerator or at room temperature for about 1 hour.

For make-ahead baking, prepare the cream cheese filling up to 2 days in advance and refrigerate it in a covered container. Let it soften at room temperature for about 20 minutes and stir well before using.

Nutrition (per serving)