Sourdough Pumpkin Cupcakes with Cream Cheese Frosting
As an Amazon Associate, I earn from qualifying purchases.
These sourdough pumpkin cupcakes are packed with fall flavor–cinnamon, ginger, nutmeg, and the rich taste of pumpkin! Use up your sourdough discard (or use active sourdough starter) to make these moist and delicious cupcakes. Top with a sweet cream cheese frosting and a sprinkle of cinnamon!
I love this time of year! The leaves, the pumpkins, the colors–all of it is just so breathtaking. Autumn makes me want to bake all the apple and pumpkin-flavored things!
I’m baking cupcakes for my sister’s upcoming baby shower, and when I asked her what flavors she would prefer, the first one she requested was pumpkin, of course! I was thrilled to get to work and conduct some recipe testing.
And I’m SO happy with how these turned out! I think you’ll love them too. The full list of ingredients, steps, and instructions is listed below!
If you’re looking for more fall-inspired desserts, check these recipes out:
- sourdough maple pecan scones
- sourdough pumpkin swirl bread
- sourdough apple cider donuts
- brown butter salted caramel cupcakes
- sourdough discard vanilla bean muffins
Step-By-Step Instructions
Prep the pans – Preheat your oven to 350°F (175°C) and line two 12-cup muffin pans with cupcake liners. You’ll have about 20 cupcakes, so leave a few cups empty if needed.
Mix the dry ingredients – In a medium bowl, whisk together the flour, baking powder, cinnamon, ginger, nutmeg, and salt until everything is evenly combined. Set aside.
Combine the wet ingredients – In a large mixing bowl, whisk the melted butter, granulated sugar, and brown sugar until smooth and glossy. Add the egg yolks and whisk again until incorporated.
Add the pumpkin mixture – Stir in the pumpkin purée, Greek yogurt, sourdough discard, and vanilla extract until the batter is creamy and well blended.
Bring it all together – Gently fold the dry ingredients into the wet ingredients using a spatula. Mix just until the flour disappears—overmixing will make the cupcakes dense.
Fill the pans – Scoop the batter evenly into the cupcake liners, filling each about ¾ full to ensure a nice domed top.
Bake – Place the pans in the oven and bake for 25 minutes, or until a toothpick inserted in the center of a cupcake comes out clean.
Cool completely – Let the cupcakes rest in the pans for 5 minutes, then transfer them to a wire rack to cool fully before frosting.
Make the frosting – Beat the softened butter and cream cheese together in a large bowl until smooth and fluffy. Mix in the vanilla, then slowly add the sifted powdered sugar, beating until light and creamy.
Frost and serve – Spread or pipe the cream cheese frosting onto the cooled cupcakes, then finish with a sprinkle of cinnamon or cinnamon stick.
Top Tips for Making these Sourdough Pumpkin Cupcakes the BEST!
- Use room-temperature ingredients – Bring the egg yolks, Greek yogurt, sourdough discard, and cream cheese to room temperature before mixing. This helps the batter blend smoothly and creates a light, tender crumb.
- Don’t overmix – Fold the dry ingredients into the wet just until the flour disappears. Overmixing can make the cupcakes dense instead of soft and fluffy.
- Use fresh sourdough discard – A recently fed discard (within a few days) adds subtle tang and depth of flavor without overpowering the pumpkin spice.
- Check early for doneness – Start testing with a toothpick at the 22-minute mark. Slightly underbaking keeps the cupcakes moist, but they should spring back lightly when touched.
- Cool completely before frosting – Let the cupcakes cool fully on a wire rack so the cream cheese frosting stays thick and doesn’t melt into the cake.
Equipment Needed
- Two 12-cup muffin pans (for about 20 cupcakes)
- Cupcake liners
- Mixing bowls (one large, one medium, and one small for frosting)
- Whisk and spatula (or wooden spoon)
- Electric mixer or stand mixer (for the frosting)
- Measuring cups and spoons
- Kitchen scale (optional, for precise measurements)
- Cooling rack
- Ice cream scoop or large spoon (for evenly portioning batter)
- Piping bag and tips (optional, if you want to pipe the frosting) I use the 1M piping tip
Storage
Room Temperature: Store unfrosted cupcakes in an airtight container at room temperature for up to 2 days. Frosted cupcakes can sit out for up to 4 hours if your kitchen is cool.
Refrigerator: Once frosted, keep cupcakes in an airtight container in the fridge for up to 4–5 days. Let them sit at room temperature for 15–20 minutes before serving so the frosting softens.
Freezer: Freeze unfrosted cupcakes for up to 3 months. Wrap each cupcake tightly in plastic wrap, then place in a freezer-safe bag or container. Thaw at room temperature, then frost before serving.
Make-Ahead Frosting: Cream cheese frosting can be made up to 3 days in advance and stored in the fridge. Beat it briefly before using to bring back a smooth, fluffy texture.
If you loved this recipe, you’ve GOT to try these sourdough oatmeal cream pies or my current favorite cupcake recipes: sourdough snickerdoodle cupcakes and brown butter salted caramel cupcakes!
Sourdough Pumpkin Cupcakes with Cream Cheese Frosting
Ingredients
For the Cupcakes
- 2 cups all-purpose flour
- 2 teaspoons baking powder
- 2 teaspoons ground cinnamon
- 1 teaspoon ground ginger
- ¼ teaspoon ground nutmeg
- ½ teaspoon salt
- 1 cup 2 sticks unsalted butter, melted
- 1 cup granulated sugar
- 1 cup brown sugar
- 2 egg yolks room temperature
- 1 cup canned pumpkin purée
- ¼ cup Greek yogurt room temperature
- ½ cup sourdough discard room temperature
- 2 teaspoons vanilla extract
For the Cream Cheese Frosting
- 1 cup 2 sticks salted butter, softened
- 8 oz cream cheese softened
- 1 teaspoon vanilla extract
- 4 cups powdered sugar sifted
Instructions
- Preheat the oven to 350°F (175°C) and line 2 12-cup muffin pans with 20 cupcake liners.
- In a medium bowl, whisk together the flour, baking powder, cinnamon, ginger, nutmeg, and salt.
- In a large mixing bowl, whisk together the melted butter, granulated sugar, and brown sugar until smooth. Add the egg yolks, pumpkin purée, Greek yogurt, sourdough discard, and vanilla, mixing until well combined.
- Gently fold the dry ingredients into the wet ingredients until just combined, being careful not to overmix.
- Divide the batter evenly among the cupcake liners, filling each about ¾ full.
- Bake for 25 minutes, or until a toothpick inserted in the center comes out clean. Allow the cupcakes to cool completely on a wire rack before frosting.
- To make the frosting, beat the softened butter and cream cheese together until smooth and creamy. Mix in the vanilla, then gradually add the powdered sugar, beating until light and fluffy.
- Spread or pipe the frosting onto the cooled cupcakes and enjoy!
These were really good! Everyone enjoyed them over here!