Sourdough Pumpkin Spice Cupcakes With Cream Cheese Frosting
Light and fluffy, this recipe for Sourdough Pumpkin Spice Cupcakes With Cream Cheese Frosting has warm and comforting notes of cinnamon, ginger, and cloves that compliments the earthy richness of pumpkin and sourdough. These simple cupcakes are topped with a maple cream cheese frosting for a fall favorite that will use up your sourdough discard!
If you’re looking for more pumpkin recipes, be sure to check out some of my other favorites like Pumpkin Spice S’More Bars, Pumpkin Buttermilk Waffles, Double Chocolate Pumpkin Cookies, Pumpkin Spice Latte Protein Brownies, Chocolate Pumpkin Pie Without Eggs, or Caramel Pumpkin Spice Snack Cake.

A Quick Look At The Recipe
- Recipe Name: Sourdough Pumpkin Spice Cupcakes With Cream Cheese Frosting
- Ready In: 35 minutes
- Makes: 24 cupcakes
- Main Ingredients: butter, pumpkin puree, pumpkin spice, cream cheese
- Flavor Profile: cozy pumpkin spice with tangy maple cream cheese frosting
- Dietary Info: no seed oils
- Difficulty: Medium
- Why You’ll Love It: reduce waste and create cozy pumpkin cupcakes with sourdough discard
Summarize & Save This Content On
Why You'll Love This Recipe
- Uses Sourdough Discard: I love recipes that use sourdough discard as I hate wasting food! These organic pumpkin cupcakes use sourdough discard and it lends a slightly tangy flavor that compliments the warm and comforting spices.
- Warm & Cozy: This recipe for Sourdough Pumpkin Spice Cupcakes with Cream Cheese Frosting are warm and cozy brown sugar pumpkin cupcakes. This light and fluffy crumb makes these homemade cupcakes a delicious mid morning treat, afternoon snack, or dessert!
- Cream Cheese Frosting: Yes, everyone loves cream cheese frosting! These are topped with a maple cream cheese frosting for that sweet and tangy combo! Adding maple syrup in addition to powdered sugar in cream cheese frosting just screams fall to me, it’s a pairing I love!
Jump to:
- A Quick Look At The Recipe
- Why You’ll Love This Recipe
- Ingredients
- Baker’s Tips for Sourdough Pumpkin Spice Cupcakes with Cream Cheese Frosting
- How to Make Sourdough Pumpkin Spice Cupcakes with Cream Cheese Frosting
- Recipe FAQ’s
- More Sourdough Discard Recipes
- Sourdough Pumpkin Spice Cupcakes With Cream Cheese Frosting
- The Bake Shop
Moist and fluffy, these pumpkin cupcakes use up sourdough discard and create an incredibly light cupcake that's perfectly spiced for fall. I add a maple cream cheese frosting on top for a sweet and tangy flavor profile that just screams fall!
This is another collab with my friend Hannah at Make It Dough! We have been doing recipe collabs for a year now, I can’t believe it! Hannah has inspired me to bake more with sourdough and I love all our sourdough discard recipes as it prevents food waste, which is a big thing for me! Some of my other favorite recipes of ours include Eggless Sourdough Molasses Cookies, Lemon Rosemary Sourdough, and Sourdough Chocolate Shortbread Cookies.
Ingredients

- All Purpose Flour: I use organic all purpose flour in these pumpkin cupcakes as opposed to cake flour because the pumpkin makes them so light and fluffy, the additional protein content of the all purpose flour gives them the right texture so they are crummy or falling apart.
- Cinnamon: I use organic Korintje cinnamon, which is my favorite variety. Check out my post the Best Cinnamon to Bake With for more info on different varieites.
- Baking Powder: Use baking powder, not soda for the best texture.
- Light Brown Sugar: I use my homemade light brown sugar, but store bought also works.
- Pumpkin: I use organic pumpkin puree for flavor and it makes these organic cupcake so incredibly moist and fluffy.
- Sourdough Discard: You can use your sourdough discard straight from the fridge in this recipe. If you don't have sourdough discard, you can still make this recipe by using 1 part water and 1 part all purpose flour. So, this would be 57 grams water and 57 grams all purpose flour, just mix together and use in ints place. It won't have the same flavor, but it will still be delicious.
- Cinnamon Sticks: I garnish these pumpkin cupcakes with organic cinnamon sticks. Totally optional, but it makes them look super cute!
*For a full list of ingredients and measurements, visit the recipe card below.
Baker's Tips for Sourdough Pumpkin Spice Cupcakes with Cream Cheese Frosting
- Always use a digital food scale for the best results.
- Make sure butter is soft, this is key for both the cupcakes and the cream cheese frosting.
- Save those extra egg whites and store in an airtight container in the fridge. You can cook them up for your dog or use in other recipes like French macarons that only call for egg whites.
- You do not need to frost these pumpkin cupcakes with a piping bag. You can easily just use a butter knife or spoon too!
- Store cupcakes under a cake dome or in an airtight container so they stay fresh. They should also be stored in the fridge because of the cream cheese frosting.
- High Altitude— Bake for 18 to 20 minutes or until a toothpick inserted in the center comes out clean.
How to Make Sourdough Pumpkin Spice Cupcakes with Cream Cheese Frosting

- Preheat the oven to 375°F. Line 2 cupcake tins with liners. To make the batter: In a large mixing bowl, add the flour, cinnamon, baking powder, ginger, sea salt, and cloves. Whisk together to combine completely and set aside.

- In the bowl of a stand mixer fitted with the paddle attachment, add the butter and light brown sugar.

- Cream together until light and fluffy.

- Add in the egg yolks, pumpkin puree, and sourdough discard.

- Mix until the starter has fully dissolved into the mixture.

- Using a spatula (or with your mixer on the low setting), slowly add in the flour mixture and mix until combined.

- Using a large spoon or cookie scoop, fill the cupcakes three-quarters full.

- Bake for 19 to 21 minutes or until a toothpick inserted in the center comes out clean.

- To make the frosting: In the bowl of a stand mixer fitted with the paddle attachment (or using a hand mixer) add the butter, cream cheese, maple syrup, and powdered sugar. Mix on low until combined, then speed mixer up to high and whip for 1 to 2 minutes or until light and fluffy. Be sure to scrape down the sides of the bowl and paddle to mix thoroughly so you have a smooth texture.

- Transfer the frosting to a piping bag with Ateco tip #827.

- To make the topping: In a small bowl, add the cane sugar and cinnamon and stir to combine completely. Be sure to have this ready before frosting the cupcakes so when you sprinkle this on top, it sticks and the frosting hasn’t began to set yet.

- Pipe frosting onto each cupcake and sprinkle with the cinnamon and sugar mixture. Stick with a cinnamon stick (optional).

Recipe FAQ's
Sourdough discard is the excess sourdough starter that is discarded during the feeding process. Instead of throwing it out, you can use it in baked goods, like these cupcakes, to give a sourdough tang flavor. It also reduces food waste!
You can mix together equal parts all purpose flour and water, 57 grams water and 57 grams all purpose flour, Just mix together and use in ints place. It won't have the same flavor, but it will still be delicious.
No way! While I usually frost cupcakes with a piping bag and decorating tip, but they are not necessary at all. It just comes naturally to me from all my commercial baking experience. But you can easily frost cupcakes with a butter knife, spatula, or spoon!
Yes, just be sure to store in the fridge because of the cream cheese frosting.
Yes, because they have cream cheese frosting.


More Sourdough Discard Recipes
Loved it? Tell us!
Thanks a waffle lot for stopping by 🧇 If you loved this recipe, sprinkle some love by leaving a ⭐⭐⭐⭐⭐ review — it inspires others to try this recipe and helps me organically reach dog loving foodies like you! I personally read and appreciate every message!
Also, be sure to subscribe to our YouTube channel and join John John and me in the kitchen for step by step recipe videos! And subscribe to our newsletter for new and seasonal recipes!

Sourdough Pumpkin Spice Cupcakes With Cream Cheese Frosting
Equipment
- Digital Food Scale
- Stand Mixer
- Cupcake Pan
- Piping Bags
- Ateco Tip #827
Ingredients
Batter
- 300 grams all purpose flour
- 2 teaspoons ground cinnamon
- 1 ½ teaspoons baking powder
- 1 teaspoon ground ginger
- ¾ teaspoon fine sea salt
- ½ teaspoon ground cloves
- 226 grams salted butter (softened)
- 400 grams light brown sugar (packed)
- 2 large egg yolks
- 425 grams pumpkin puree
- 113 grams sourdough discard
Frosting
- 226 grams salted butter (softened)
- 113 grams cream cheese
- 88 grams maple syrup
- 566 grams powdered sugar (sifted)
Topping
- 1 tablespoon cane sugar
- Pinch of ground cinnamon
- cinnamon sticks (optional)
Instructions
- Preheat the oven to 375°F. Line 2 cupcake tins with liners.
- To make the batter: In a large mixing bowl, add the flour, cinnamon, baking powder, ginger, sea salt, and cloves. Whisk together to combine completely and set aside.
- In the bowl of a stand mixer fitted with the paddle attachment, add the butter and light brown sugar. Cream together until light and fluffy. Mix in the egg yolks, pumpkin puree, and sourdough discard until the starter has fully dissolved into the mixture.
- Using a spatula (or with your mixer on the low setting), slowly add in the flour mixture and mix until combined.
- Using a large spoon or cookie scoop, fill the cupcakes three-quarters full.
- Bake for 19 to 21 minutes or until a toothpick inserted in the center comes out clean.
- To make the frosting: In the bowl of a stand mixer fitted with the paddle attachment (or using a hand mixer) add the butter, cream cheese, maple syrup, and powdered sugar. Mix on low until combined, then speed mixer up to high and whip for 1 to 2 minutes or until light and fluffy. Be sure to scrape down the sides of the bowl and paddle to mix thoroughly so you have a smooth texture.
- Transfer the frosting to a piping bag with Ateco tip #827.
- To make the topping: In a small bowl, add the cane sugar and cinnamon and stir to combine completely. Be sure to have this ready before frosting the cupcakes so when you sprinkle this on top, it sticks and the frosting hasn’t began to set yet.
- Pipe frosting onto each cupcake and sprinkle with the cinnamon and sugar mixture. Stick with a cinnamon stick (optional).
- Store in an airtight container in the fridge for up to 3 days.
Video
Notes
- Always use a digital food scale for the best results.
- Make sure butter is soft, this is key for both the cupcakes and the cream cheese frosting.
- Save those extra egg whites and store in an airtight container in the fridge. You can cook them up for your dog or use in other recipes like French macarons that only call for egg whites.
- You do not need to frost these pumpkin cupcakes with a piping bag. You can easily just use a butter knife or spoon too!
- Store cupcakes under a cake dome or in an airtight container so they stay fresh. They should also be stored in the fridge because of the cream cheese frosting.
- High Altitude— Bake for 18 to 20 minutes or until a toothpick inserted in the center comes out clean.
Nutrition
The Bake Shop
Visit The Bake Shop for foodie inspired tees, sweatshirts, and accessories. Find my favorite kitchen tools (with discounts!) in the Kitchen Shop. And shop our collection of food inspired dog accessories too!









So fluffy and perfectly spiced!
These cupcakes are incredible! Excellent flavor, so fluffy, and the spice is to die for! My kids even loved them! Will definitely bake them again soon!