Pumpkin Cream Cheese Muffins
Published Oct 07, 2026
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These pumpkin cream cheese muffins are moist, spiced pumpkin muffins swirled with sweet cream cheese filling. Topped with toasted pecans for a crunchy finish, they’re a perfect fall breakfast treat.
Cream Cheese Swirled Pumpkin Muffins
Has anyone else’s craving for fall baking kicked in yet? Every year, I start dreaming of pumpkin spice before the first leaf hits the ground. Very soon after, it’s on to recipes like pumpkin protein muffins, pumpkin bars, chocolate pumpkin bread, and these irresistible cream cheese-swirled pumpkin muffins.
All those cozy spices and rich, pumpkin cheesecake-like flavors put these moist, tender muffins firmly at the top of my seasonal to-bake list. After today, I think they’ll be on yours, too.
What I Love Most About These Pumpkin Cream Cheese Muffins
- They’re filled with warm flavors of pumpkin spice, brown sugar, and maple syrup.
- Made with melted butter instead of oil for extra richness and flavor.
- They stay soft for days due to the Greek yogurt in the recipe.
- The sweet, tangy cheesecake swirl that tastes just like the filling in my sweet potato cookies. You don’t need to hollow out the muffins to fill them; just swirl it right in.
- It’s the closest thing to eating dessert for breakfast this fall!
Ingredients Needed
Gather up the following ingredients to make these decadent pumpkin cheesecake muffins. See the recipe card for exact measurements.
- Cream Cheese – Use a cream cheese brick (not the kind that comes in a tub) and bring it to room temperature.
- Egg Yolk – Adding an egg yolk helps to stabilize and enrich the sweet cream cheese filling. It’s easiest to separate the yolk while the egg is cold from the fridge.
- Vanilla – For a fun variation, swap half of the vanilla extract with maple extract.
- Flour – Use all-purpose flour, spooned and leveled, or weigh the flour using a kitchen scale.
- Baking Powder and Baking Soda – Using both gives the muffins extra lift.
- Spices – I like to supplement pumpkin pie spice with extra cinnamon and ginger. You can also replace the pie spice with a blend of ground cinnamon, nutmeg, ginger, and cloves.
- Pumpkin Purée – Not to be confused with canned pumpkin pie filling. Make sure to buy 100% pure pumpkin, without spices or sweeteners.
- Whole Eggs – Bring them to room temperature.
- Greek Yogurt – Yogurt makes these muffins moist. Sour cream is a good substitute.
- Butter – Melted and cooled. I prefer the flavor of butter over oil in my muffin recipes. You can use vegetable oil if you need to.
- Brown Sugar – I recommend regular brown sugar or light brown sugar.
- Maple Syrup – Make sure to use real maple syrup, not pancake syrup. If you don’t have maple syrup, substitute another liquid sweetener like honey.
- Chopped Pecans – Optional, for topping the muffins. I toast the pecans in a dry skillet or in the oven for a few minutes to bring out their flavor. You can also use walnuts or almonds, or leave off the nuts for a nut-free version.
Tips for Bakery-Worthy Muffins
- Use room temperature ingredients. Bring fridge-cold ingredients like cream cheese, yogurt, and eggs to room temperature before you start. This makes the ingredients easier to mix.
- Don’t overmix. Fold the wet and dry ingredients together just until no streaks of flour remain. Overmixing leads to dense muffins instead of light, tender ones.
- Toast the pecans. For more flavor and crunch, toast the pecans in a skillet for a couple of minutes before you chop them.
- Test that the muffins are done with a toothpick, avoiding the cream cheese swirl. It should come out of the pumpkin portion mostly clean, or with a few moist crumbs.
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Pumpkin Cream Cheese Muffins
These pumpkin cream cheese muffins are moist, spiced pumpkin muffins swirled with cream cheese filling and topped with toasted pecans.
Ingredients
Cream Cheese Swirl:
- 8 ounces cream cheese, softened
- 3 tablespoons granulated sugar
- 1 large egg yolk
- 1 teaspoon pure vanilla extract
Pumpkin Muffins:
- 1¾ cups all-purpose flour
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ¼ teaspoon salt
- 2½ teaspoons pumpkin pie spice
- ½ teaspoon ground cinnamon
- ½ teaspoon ground ginger
- 1 cup pumpkin puree
- 2 large eggs, room temperature
- ½ cup plain Greek yogurt
- ¼ cup unsalted butter, melted and slightly cooled
- ⅓ cup light brown sugar, packed
- ¼ cup maple syrup
- 1 teaspoon pure vanilla extract
Topping:
- ⅓ cup finely chopped pecans
Instructions
- Prep. Preheat the oven to 375˚F. Line a 12-cup muffin pan with paper liners and set aside.
- Make the cream cheese swirl. In a mixing bowl, beat the cream cheese, sugar, egg yolk, and vanilla with an electric mixer until completely smooth. Set aside.
- Combine the dry ingredients. In a large bowl, whisk together the flour, baking powder, baking soda, salt, pumpkin pie spice, cinnamon, and ginger.
- Combine the wet ingredients. In another bowl, whisk together the pumpkin puree, eggs, Greek yogurt, melted butter, brown sugar, maple syrup, and vanilla until smooth.
- Make the muffin batter. Add the wet ingredients to the dry ingredients and gently fold until just combined. Do not overmix.
- Fill the muffin cups. Divide the batter evenly among the muffin cups, filling each about ⅔ full. Spoon about 1½ tablespoons of the cream cheese mixture onto each muffin. Using a toothpick or skewer, gently swirl it into the batter with just 2–3 passes. Sprinkle with the chopped pecans.
- Bake. Transfer to the oven and bake the muffins for 20–24 minutes, or until the pumpkin portion is set and a toothpick inserted into the muffin (avoiding the cream cheese swirl) comes out with a few moist crumbs.
- Serve. Remove the pumpkin muffins from the oven and let them cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely before serving.
Equipment
Notes
- Bring the cream cheese to room temperature before mixing so you get a nice, smooth swirl.
- Avoid overmixing the batter to keep the muffins light, moist, and tender.
Nutrition
Serving: 1muffin | Calories: 254kcal | Carbohydrates: 27g | Protein: 6g | Fat: 14g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Trans Fat: 0.2g | Cholesterol: 73mg | Sodium: 172mg | Potassium: 171mg | Fiber: 2g | Sugar: 11g | Vitamin A: 3614IU | Vitamin C: 1mg | Calcium: 68mg | Iron: 2mg
Nutritional info is an estimate and provided as courtesy. Values may vary according to the ingredients and tools used. Please use your preferred nutritional calculator for more detailed info.
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How to Make Pumpkin Cream Cheese Muffins
Be prepared for the whole kitchen to smell like a pumpkin spice latte!
- Prepare the cream cheese swirl. Begin by beating the cream cheese with sugar, egg yolk, and vanilla to make the cream cheese filling.
- Mix the dry ingredients. Next, whisk together the flour, baking powder, baking soda, salt, and spices.
- Make the muffin batter. Separately, combine the pumpkin puree, eggs, Greek yogurt, melted butter, brown sugar, maple syrup, and vanilla, and mix until smooth. Gently fold the wet mixture into the dry mixture.
- Swirl the muffins. Now, divide the batter evenly between the lined wells of a muffin pan (fill each liner about ⅔ full). Top each muffin with 1½ tablespoons of the cream cheese filling, then swirl it in using a toothpick or skewer. I usually do 2-3 passes. Sprinkle the tops with chopped pecans (optional).
- Bake. Pop them in the oven and bake these pumpkin muffins at 375ºF for 20-24 minutes, until they’re set. Cool the muffins in the pan for a few minutes, then move them to a wire rack to cool completely before storing or serving.
Storage
- Store covered at room temperature. Let the muffins cool completely to room temperature before storing them in an airtight container. They’ll last at room temperature for 2-3 days. For longer-term storage, I recommend refrigerating or freezing.
- Freeze. Freeze these pumpkin cheesecake muffins for up to 1 month. Thaw at room temperature before serving.
