Sourdough Pumpkin Cookies

Every fall, my kids and I bake a version of these Sourdough Pumpkin Cookies for their little cookie business, and they’ve become a customer favorite year after year. Soft pumpkin cookies made with sourdough discard have incredible depth of flavor, and the smooth cream cheese center in this pumpkin cookie recipe melts right into every bite.

They’re festive, perfectly spiced, and just the right balance of sweet and tangy which makes them ideal for sharing at fall gatherings or pairing with a warm mug of apple cider. If you’re looking for an easy pumpkin dessert that uses sourdough discard, this is one you’ll bake again and again. And for even more inspiration, explore my collection of fall sourdough recipes filled with pumpkin-spice sourdough favorites.

Why You’ll Love Sourdough Pumpkin Cookies

• Creamy Filling – These sourdough cookies are filled with a smooth cream cheese center that melts into every bite. It’s the perfect sweet-tangy balance, and my tips make the filling easy and mess-free to add. For other filled pumpkin favorites, try my Sourdough Pumpkin Roll and Sourdough Pumpkin Scones too!
• Pumpkin Flavor – Pumpkin in the dough makes these cookies incredibly soft, while the baking method keeps the edges slightly crisp. It’s the perfect texture in a cookie—soft in the middle with just the right amount of chew, like my show-stopping Sweet Pumpkin Sourdough Focaccia.
• Fall Treat – If you love my Pumpkin Bars with Sourdough Discard, these pumpkin cookies will be your new go-to. They’re festive, easy to make, and the perfect sweet to bake and share all fall long.

Sourdough Discard Tip: I keep a jar in my fridge that I continually add sourdough discard to. Discard is a by-product of your sourdough starter and there is no reason to throw it away. Instead, use it in incredible sourdough discard recipes where it adds moisture and great flavor. Use older, more tangy discard in savory recipes like my Sourdough Discard French Bread and young/fresh discard in sweeter recipes like these Healthy Sourdough Pumpkin Muffins.

Important Ingredients

• Sourdough Discard – I like to use a young discard or even a fresh, active starter in these cookies. If your discard is older and more runny, you may need to add a bit of extra flour to the dough. I always use 100% hydration sourdough discard (starter that has been fed equal weights flour and water) for consistent results.
• Cream Cheese Filling – The sweet cream cheese filling is made with cream cheese, powdered sugar, vanilla, and a hint of cinnamon. Mix it up first so you can chill it in the freezer while preparing your cookie dough—it makes assembly easy and mess-free.
• Pumpkin Puree – I like to use canned pumpkin (not pumpkin pie filling) for consistent results. If you use homemade pumpkin puree, you will need to add a bit of extra flour to balance the extra moisture (it’s much more liquid-y than canned pumpkin). The dough should feel soft but not overly wet or sticky. If it does, that’s your sign to add a little more flour.
• Spices – A mix of pumpkin pie spice and cinnamon brings all the warm fall flavor you’d expect from a pumpkin cookie. The spices pair perfectly with the tangy cream cheese center and make every bite taste like fall.
• Pumpkin Spice Sugar Mixture – After shaping the cookies, they’re rolled in a blend of sugar and pumpkin pie spice, giving them that irresistible snickerdoodle-like coating, similar to my Sourdough Snickerdoodles.

See the recipe card for full information on ingredients and quantities

How to Make Sourdough Pumpkin Cookies

Prepare the Cream Cheese Filling

Step 1: In a small bowl, whip together the cream cheese, powdered sugar, vanilla, and cinnamon for a minute or two, until the mixture is smooth and creamy. Scoop it into a piping bag and pipe 18 little mounds onto a parchment paper lined baking sheet, about 1 – 1 1/2 Tablespoons each. Place the tray in the freezer while you mix up the cookie dough.

Note: The filling should release easily from the parchment once it’s firm. Depending on how warm your ingredients were to start, it might take a little more or less time, but I recommend giving it at least 30 minutes in the freezer.

Mix the Cookie Dough

Step 2: In a medium mixing bowl, whisk together the all-purpose flour, baking powder, baking soda, salt, ground cinnamon and pumpkin pie spice. Set aside.

Step 3: In a large mixing bowl, beat the unsalted butter with a hand mixer until light and fluffy. Add the brown sugar and granulated sugar and cream together with the butter until smooth. Mix in the sourdough discard, then add the canned pumpkin and vanilla extract, beating until fully incorporated.

Step 4: Add dry ingredients to the wet ingredients, beating the mixture together until a cohesive dough is formed.

The dough should be workable without being too sticky.

Sticky Cookie Dough? Depending on the hydration of your sourdough discard (older discard is often more “liquidy”) and the moisture level in your canned pumpkin (homemade pumpkin is VERY wet), you may need to adjust the flour slightly. Add a little more or less until the dough holds its shape and isn’t too sticky.

Shape & Stuff the Cookie Dough

Step 5: Use a cookie scoop to scoop 18 cookie dough balls, about 2 Tbsp per ball.

Step 6: Make an indent on each cookie with your thumb and remove the filling from the freezer.

Step 7: Working quickly, place one ball of frozen cream cheese filling into the center of each dough ball. Roll the dough around the filling to fully seal it before the cream cheese begins to thaw.

Step 8: Roll each ball of dough in a pumpkin spice sugar mixture and place on a parchment lined baking sheet, about 8-9 to a pan.

Amy’s Cookie Tip: Try to position the cream cheese filling in the center or slightly toward the top of the dough ball. This leaves space at the bottom for the cookie to spread as it bakes.

Bake the Pumpkin Cookies

Step 9: Bake sourdough pumpkin cookies at 400°F (convection) for 10 minutes.

Step 11: Allow the cookies to cool on the baking sheet until mostly set before transferring to a wire rack to cool. Enjoy!

Convection Baking Tip: For the best texture (crispy edges with a soft center), bake at 400°F using the convection setting. If your oven doesn’t have convection, preheat it well and bake at 400°F for 1–2 minutes longer. A full preheat helps the cookies set properly and get those golden, slightly crisp edges.

How to Store Leftovers

Because these cookies have a cream cheese filling, they should be refrigerated or frozen. They can sit at room temperature for up to 1–2 hours, but for best freshness, freeze them once cooled. The refrigerator can dry out baked goods, so the freezer is the better option to keep them soft and flavorful. Let the cookies sit at room temperature for about 30 minutes before serving.

Make Ahead Tip: The cookie dough can also be frozen after adding the cream cheese filling. When ready to bake, transfer the dough balls to the refrigerator and let them thaw overnight before baking as directed.

Frequently Asked Questions

Easy Sourdough Pumpkin Treats

Sourdough Pumpkin Muffins

Sourdough Pumpkin Bread

Pumpkin Bars with Sourdough Discard

Sourdough Pumpkin Scones

If you tried these Sourdough Pumpkin Cookies or any other recipe on my website leave a 🌟 star rating and let me know how it went in the comments below. Happy Baking!