These Sourdough Pumpkin Cream Cheese Muffins are soft, spiced, and filled with cozy fall flavor. A swirl of sweet cheesecake filling runs through the pumpkin muffin base, creating a bakery-style treat with beautiful color and flavor.
Made with sourdough discard, these muffins have a subtle tang and extra moisture that makes them irresistibly soft. They're easy enough for weekday mornings but special enough for a fall brunch or gathering.
These muffins are made for crisp fall days and cozy sweater weather. Bake them in October or November when pumpkin is at its peak and your kitchen is begging to smell like cinnamon and nutmeg.
They also make a beautiful addition to Thanksgiving breakfast spreads, back-to-school treats, or even Halloween weekend baking.
If you love these Sourdough Pumpkin Cream Cheese Swirl Muffins, try my Pumpkin Banana Muffins and my Sourdough Cinnamon Rolls—they’re warm, comforting, and perfect for fall mornings.
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Ingredients
For the Muffins
- All-purpose flour
- Baking powder
- Baking soda
- Kosher salt
- Pumpkin pie spice
- Brown sugar
- Granulated sugar
- Sourdough discard
- Pumpkin purée
- Neutral oil
- Eggs
- Vanilla extract
For the Cream Cheese Filling
- Cream cheese
- Granulated sugar
- Vanilla extract
Optional Topping
- Coarse sugar or cinnamon sugar
See recipe card for quantities.
Four-Step Overview
Note: I bake by weight for accuracy. Cup measurements are approximate and may vary depending on how you scoop.
Step 1: Make the cream cheese filling: Beat cream cheese, sugar, and vanilla until smooth.
Step 2: Mix the batter: Whisk wet ingredients, fold in dry ingredients, and stir until just combined.
Step 3: Assemble: Fill muffin cups with batter, swirl in cream cheese filling. The liners will be just about filled to the top.
Step 4: Bake: Top with cinnamon sugar and bake at 425°F for 5 minutes, then at 350°F until set.
Weigh your ingredients! Using a kitchen scale ensures your measurements are accurate, which is key for getting consistent results in baking. It takes the guesswork out of measuring and helps your recipes turn out exactly as intended every time.
Substitutions
- Pumpkin purée: Canned or homemade pumpkin both work well—just avoid using pumpkin pie filling.
- Sourdough discard: You can substitute with plain Greek yogurt or sour cream if needed (use 100g).
- Spices: Use pumpkin pie spice or a mix of cinnamon, nutmeg, and ginger.
- Cream cheese: Both block-style and whipped cream cheese will work—just soften it first for easy swirling.
Variations
- Add chocolate chips: Stir ½ cup mini chocolate chips into the batter for a chocolate-pumpkin combo.
- Make it loaf-style: Bake the batter in a greased 8x4-inch loaf pan with the cream cheese swirled on top (increase baking time).
- Top with streusel: Add a cinnamon crumb topping before baking for extra crunch and sweetness.
Equipment
- Kitchen scale
- 12-cup muffin tin
- 3-tablespoon cookie scoop (for scooping batter into the muffin liners)
- Parchment muffin liners or nonstick spray
- Medium mixing bowl (for dry ingredients)
- Large mixing bowl (for batter)
- Small bowl (for cream cheese filling)
- Whisk
- Spatula
- Electric hand mixer or stand mixer (for cream cheese filling)
- (I used a fork and it worked great)
- Measuring spoons
- Toothpick or butter knife (for swirling)
- Measuring spoons
Storage
Store the muffins in an airtight container in the fridge for up to 4–5 days. Let them come to room temperature or warm slightly before eating for the best texture.
To freeze, wrap each muffin individually and store in a freezer-safe bag or container for up to 2 months. Thaw overnight or microwave gently before serving.
Audrey's Tip
For gooier cream cheese pockets, dollop the cream cheese in the center without swirling too much. For a more “coffee shop swirl” look, drag a toothpick through the cream cheese in a figure-eight pattern.
Related
Looking for other recipes like this? Try these:
Sourdough Pumpkin Cream Cheese Muffins
Ingredients
For the muffins:
- 250 g all-purpose flour 2 cups
- 1 ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon kosher salt
- 1 ½ teaspoon pumpkin pie spice
- 100 g brown sugar packed (½ cup)
- 75 g granulated sugar ⅓ cup
- 120 g sourdough discard unfed (½ cup)
- 240 g pumpkin purée 1 cup
- 120 ml neutral oil ½ cup
- 2 large eggs room temperature
- 1 teaspoon vanilla extract
For the cream cheese filling:
- 113 g cream cheese softened (4 oz)
- 30 g granulated sugar 2 tbsp
- ½ teaspoon vanilla extract
Optional topping:
- Coarse sugar or cinnamon sugar for sprinkling
Instructions
- Prep the oven & pan: Preheat oven to 425°F (220°C). Line a 12-cup muffin tin with parchment liners or grease well.
- Make the cream cheese filling: In a small bowl, beat cream cheese, sugar, and vanilla until smooth and fluffy. Set aside. You can use a mixer for this, but I used a fork and it worked just fine. Just make sure your cream cheese is nice and soft!
- Mix the dry ingredients: In a medium bowl, whisk together flour, baking powder, baking soda, salt, and pumpkin pie spice.
- Make the batter: In a large bowl, whisk together brown sugar, granulated sugar, sourdough discard, pumpkin purée, oil, eggs, and vanilla until smooth. Gently fold in the dry ingredients until just combined.
- Assemble the muffins: Fill each muffin cup about ⅔ full with batter. Spoon about 1 teaspoon of cream cheese mixture on top of each and gently swirl with a toothpick or butter knife. Add a bit more batter on top if desired, then sprinkle with coarse or cinnamon sugar.
- Bake: Bake at 425°F for 5 minutes, then reduce oven temperature to 350°F (175°C) and bake for an additional 15–18 minutes, until a toothpick inserted into the muffin (not the cream cheese) comes out clean.
- Cool & serve: Let muffins cool in the pan for 5 minutes before transferring to a wire rack. Best enjoyed warm!
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