Sourdough Pumpkin Cream Cheese Muffins (with oat crumble!)
It’s that time of year that we all wait for! Pumpkin season is upon us, and I can’t think of any better way to embrace the season than to whip up a batch of these Sourdough Pumpkin Cream Cheese Muffins (with oat crumble!). That one very popular coffee chain has made these muffins a viral sensation, and I’m here to show you how to make them for half the cost and with your starter!
Why You’ll Love This Recipe:
These muffins seriously deliver on pumpkin spice flavor and that creamy cheesecake center makes them even more decadent. Mix up a simple oat crumble topping to add crunch to the top, and you’ll be in pumpkin heaven. Perfect for fall baking and with an optional overnight fermentation step, these muffins aren’t just delicious- they’ll fit your busy schedule and be easy on the stomach with the extra fermentation.
Why Use Sourdough Starter in Muffins?
Using sourdough discard in muffins adds a slight tang, enhances moisture retention, and makes the crumb softer and more tender. The fermentation process also helps break down gluten, making these muffins easier to digest.
Do I have to long-ferment these Muffins?
No! You can mix up this batter if you want muffins quickly. Just skip the fermentation step!
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Tools You’ll Need:
• Standard 12-cup muffin tin- for baking muffins. I love these pans from USA Bakeware linked here.
• Muffin liners- to avoid burned edges. I love these bakery style parchment muffin liners linked here.
• Kitchen scale (optional)– for accurate measuring, especially helpful with sourdough baking.
• 1/4 cup scoop – for scooping batter. I love this scoop for muffins linked here.
• Whisk + spatula- for combining ingredients.
• Mixing bowls- for mixing batter, crumble, and cream cheese filling.
• Hand mixer or sturdy whisk- for mixing batter and filling.
• Cooling rack– to cool muffins.
• Pastry bag or ziplock- for piping cream cheese filling.
• Pastry filling tip (optional)- I use this set of tips for filling muffins and cupcakes! It’s not necessary but great if you plan to make a lot of these. I’ve linked the set I use here.
Gather Your Ingredients:
Pumpkin Puree– Brings natural sweetness, moisture, and tenderness to the muffins, while giving the muffins that classic pumpkin flavor we want!
Avocado Oil- Adds moisture and keeps the muffins soft and tender. You can substitute for any neutral cooking oil.
Sour Cream– Adds moisture and tang to balance sweetness and enhance tenderness of the crumb. You can also substitute for full-fat Greek yogurt.
Brown sugar– Helps to sweeten the muffins and gives that fall flavor from the molasses. Used in the crumble too.
White sugar– Boosts sweetness and supports the rise and golden color.
Vanilla extract- Enhances the flavor and brings warmth.
Salted butter– Binds the crumble to give it crisp buttery texture.
Sourdough starter- (flat or past peak, can be cold or room temperature). Adds depth of flavor, moisture, and just a whisper of tang—without making these muffins “sour”. Key for fermentation.
Eggs (room temperature)– provide structure and lift with moisture, works as a binder for ingredients.
All-purpose flour- Gives the bread structure while keeping it soft and cakey. You’ll also use flour in the oat crumble.
Baking powder + Baking soda– Ensures the right rise and bakery-style domes for the muffins.
Salt- Balances sweetness and enhances all the other flavors.
Cinnamon, Ginger, Nutmeg, and Cardamom- Rounds out the pumpkin flavor and brings that classic pumpkin spice warmth. You can substitute these spices for a pumpkin spice blend of you prefer, but I like to mix my own to guarantee the flavor is the same each time.
Cream Cheese– make sure to use cream cheese and not a spread for the filling.
Powdered Sugar- sweetens and stabilizes the cream cheese filling.
Rolled Oats- Gives texture and crunch to the oat topping.
Now let’s bake!
Instructions
Step 1: Mix the Batter
In a large mixing bowl, whisk together the egg, egg yolk, Greek yogurt, sourdough discard, white sugar, brown sugar, vanilla, pumpkin purée, and oil until smooth.
In a medium bowl, whisk together flour, cinnamon, ginger, nutmeg, cardamom, baking soda, baking powder, and salt.
Add dry ingredients to wet. Beat wet ingredients with a whisk or a hand mixer until everything is well combined. Do not overmix.
Overnight Fermentation: Cover tightly with plastic wrap and refrigerate for 8–12 hours for added fermentation benefits. If baking same day, skip this step.
Step 2: Make Oat Crumble
This topping is TO DIE FOR, so don’t skip it! In a small bowl, melt the butter for your crumble. Add rolled oats, brown sugar, flour, cinnamon, ginger, and nutmeg to the bowl. Combine with a spoon or fingers until a crumbly mixture forms. Set aside for later.
Step 3: Make Cream Cheese Filling
Make sure your cream cheese is room temperature and soft. Transfer to a bowl, and add powdered sugar. Beat with hand mixers on high for about a minute, you want the filling to be light and creamy. If you’re using a pastry tip, fit a pastry bag with the tip. Transfer all of the filling to a pastry bag or a ziplock bag. Cut off 1/4 inch of the corner end of the ziplock or pastry bag.
Step 3: Assemble and Bake
Preheat oven to 350°F. Line a 12-cup muffin pan with parchment liners, and gently spray with cooking spray to avoid sticking.
If batter was fermented overnight, allow to rest 30 minutes at room temperature and gently fold with a spatula to combine ingredients.
In each muffin cup, spoon 1/4 cup of batter into the muffin tins.
Grab your bag filled with cream cheese filling, and stick the bag with the end cut off down into the center of the muffin. Pipe down into the muffin and squeeze, pulling up with the bag to form a circle on the top of the muffin as pictured below. You should be piping about 2 teaspoons of filling into each center.
Sprinkle a spoonful of the oat topping around the edges of the muffins, making sure not to put the crumble on top of the cream cheese.
Place the muffins in the oven and bake at 350°F for 25-28 minutes. You want the edges to feel firm and the cheesecake center should look set. Remove muffins when done baking from the oven.
Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling.
Enjoy!
Yields 12 muffins
How to Store:
Room Temperature- Store muffins in an airtight container on counter for up to 1 day.
Refrigerator- store in an airtight container for up to 3 days. Gently warm before serving.
FAQ’S:
Can I make these without the overnight fermentation?
Absolutely. They’ll still be moist and flavorful baked right away, but fermentation deepens the flavor and improves rise.
Can I use canned pumpkin pie mix?
No, it already contains sugar and spices, which will throw off the balance of the recipe. Use pure pumpkin purée.
Drop a comment and leave a review if you loved this recipe! Happy baking!
Sourdough Pumpkin Cream Cheese Muffins (with oat crumble!)
Equipment
- 12-cup muffin tin – for baking muffins.
- Muffin liners – for lining tin to avoid burning.
- Kitchen scale (optional)
- 1/4 cup scoop – for scooping muffin batter.
- Whisk – for mixing batter.
- Spatula
- Mixing bowls – for batter, crumble, and filling.
- Hand mixer – for cream cheese filling.
- Cooling rack – for cooling muffins.
- Pastry bag or ziplock – for piping filling.
- Pastry tip (optional)
Ingredients
Sourdough Pumpkin Cream Cheese Muffins
Wet Ingredients:
- 1 large egg
- 1 egg yolk
- 2 tbsp (30g) plain full-fat Greek yogurt
- ⅓ cup (80g) sourdough discard
- 1 tsp vanilla extract
- ¾ cup (180g) pumpkin purée
- ⅓ cup (75g) avocado or neutral oil
- ½ cup (100g) white sugar
- ¼ cup (50g) light brown sugar
Dry Ingredients:
- 1¾ cups (220g) all-purpose flour
- 2 tsp ground cinnamon
- ½ tsp ground ginger
- ½ tsp ground nutmeg
- ⅛ tsp ground cardamom
- 1 tsp baking soda
- 1½ tsp baking powder
- ¾ tsp fine sea salt
Oat Crumble:
- 4 Tablespoons (57g) melted salted butter
- 1/2 cup (50g) rolled oats
- 1/2 cup (100g) brown sugar
- 1 1/2 teaspoon cinnamon
- 1/4 teaspoon ginger
- 1/4 teaspoon nutmeg
- 1/8 teaspoon cardamom (optional)
Cream Cheese Filling:
- 6 oz (170g) cream cheese softened
- 3 Tablespoons (24g) powdered sugar
Instructions
Step 1: Mix the Batter
- In a large mixing bowl, whisk together the egg, egg yolk, Greek yogurt, sourdough discard, white sugar, brown sugar, vanilla, pumpkin purée, and oil until smooth.1 large egg, 1 egg yolk, 2 tbsp (30g) plain full-fat Greek yogurt, ⅓ cup (80g) sourdough discard, 1 tsp vanilla extract, ¾ cup (180g) pumpkin purée, ⅓ cup (75g) avocado or neutral oil, ½ cup (100g) white sugar, ¼ cup (50g) light brown sugar
- In a medium bowl, whisk together flour, cinnamon, ginger, nutmeg, cardamom, baking soda, baking powder, and salt.1¾ cups (220g) all-purpose flour, 2 tsp ground cinnamon, ½ tsp ground ginger, ½ tsp ground nutmeg, ⅛ tsp ground cardamom, 1 tsp baking soda, 1½ tsp baking powder, ¾ tsp fine sea salt
- Add dry ingredients to wet. Beat wet ingredients with a whisk or a hand mixer until no streaks remain. Do not overmix.
- Overnight Fermentation: Cover tightly with plastic wrap and refrigerate for 8–12 hours for added fermentation benefits. If baking same day, skip this step.
Step 2: Make Oat Crumble
- This topping is TO DIE FOR, so don’t skip it! In a small bowl, melt the butter for your crumble. Add rolled oats, brown sugar, flour, cinnamon, ginger, and nutmeg to the bowl. Combine with a spoon or fingers until a crumbly mixture forms. Set aside for later.4 Tablespoons (57g) melted salted butter, 1/2 cup (50g) rolled oats, 1/2 cup (100g) brown sugar, 1 1/2 teaspoon cinnamon, 1/4 teaspoon ginger, 1/4 teaspoon nutmeg, 1/8 teaspoon cardamom
Step 3: Make Cream Cheese Filling
- Make sure your cream cheese is room temperature and soft. Transfer to a bowl, and add powdered sugar. Beat with hand mixers on high for about a minute, you want the filling to be light and creamy. If you’re using a pastry tip, fit a pastry bag with the tip. Transfer all of the filling to a pastry bag or a ziplock bag. Cut off 1/4 inch of the corner end of the ziplock or pastry bag.6 oz (170g) cream cheese, 3 Tablespoons (24g) powdered sugar
Step 3: Assemble and Bake
- Preheat oven to 350°F. Line a 12-cup muffin pan with parchment liners, and gently spray with cooking spray to avoid sticking.
- If batter was fermented overnight, allow to rest 30 minutes at room temperature and gently fold with a spatula to combine ingredients.
- In each muffin cup, spoon 1/4 cup of batter into the muffin tins.
- Grab your bag filled with cream cheese filling, and stick the bag with the end cut off down into the center of the muffin. Pipe down into the muffin and squeeze, pulling up with the bag to form a circle on the top of the muffin as pictured below. You should be piping about 2 teaspoons of filling into each center.
- Sprinkle a spoonful of the oat topping around the edges of the muffins, making sure not to put the crumble on top of the cream cheese.
- Place the muffins in the oven and bake at 350°F for 25-28 minutes. You want the edges to feel firm and the cheesecake center should look set. Remove muffins when done baking from the oven.
- Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling.
- Enjoy!
