It’s pumpkin season, and sourdough pumpkin cookies are the perfect fall dessert! Warm spices, fresh pumpkin, and a nutty flavor will make this one of your absolute favorite autumn sourdough recipes!
The base of this recipe has been in my recipe cards for probably 20 years. My best friend passed it along to me, but I have no idea where it came from originally. Without a doubt, I have loved making it every year! I keep changing it and adding to it each year and eventually it became this unbelievable sourdough recipe with freshly milled flour and a soft, cakey texture. It’s similar to the original recipe, but with my changes it has become a whole food autumn dessert that can actually be called healthy pumpkin cookies!
Seeing that I love all things pumpkin, this recipe is such a great way to give a pumpkin lover a cookie that is full of fall flavor, and uses gut healthy sourdough and vitamin and fiber rich freshly milled flour. Of course, if you don’t mill your own grains, this makes a perfect cookie if you choose to use all purpose flour, so don’t worry!
If you’re a pumpkin lover like me, you can also try my sourdough pumpkin cinnamon rolls and my sourdough pumpkin waffles for the best fall breakfast flavors!!
*note: these are not chewy cookies like a regular chocolate chip cookies. They are soft and delicate and cakey, more like a sourdough pumpkin bread. Undeniably, this will be one of your new favorite pumpkin recipes!
Ingredients for sourdough pumpkin cookies
Dry Ingredients
- Pinch salt
- 200g (1 cup) brown sugar (you can substitute white sugar if that’s all you have)
- 10g (2 teaspoons) baking powder
- 7g (1 teaspoon) baking soda
- 240g (2 cups) freshly milled soft white wheat, spelt or einkorn (you can also substitute all purpose flour and it works perfectly)
- 3g (1 teaspoon) cinnamon (for extra pumpkin pie flavor you can substitute pumpkin pie spice)
Wet Ingredients
- 1 room temperature egg
- 8g (1 teaspoon) vanilla extract
- 70g (1/4 cup) sourdough discard or active starter
- 1 small 15oz can of pumpkin puree (be very sure you are not using pumpkin pie filling)
- 1/2 stick unsalted butter, melted (can substitute a neutral tasting oil)
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Add Ins for sourdough pumpkin cookies
- 200-400g (1-2 cups) dark chocolate chips
Instructions for sourdough pumpkin chocolate chip cookies:
In the following recipe, I provide regular measurements, as well as scale weight. I think it’s well worth it to purchase an inexpensive kitchen scale to make sure your baked goods have a consistency to them by always having the correct measurement of ingredients. While I use scale weights now, I grew up in a measuring cup / teaspoon household so I’ve provided both. In either case, you’ll end up with delicious sourdough pumpkin chocolate chip cookies!
1. Combine wet ingredients
In a small bowl, combine wet ingredients – room temperature egg, vanilla extract, sourdough starter discard (or active sourdough starter), pumpkin puree.
2. Combine dry ingredients
In a large bowl, combine dry ingredients – salt, brown sugar, baking powder, baking soda, freshly milled flour (or all purpose flour), and cinnamon. NOTE: for a richer fall flavor, you can add pumpkin spice to add a depth of flavor and a taste of warm spices.
*I use a Mockmill 200 to grind my wheat berries. You do not need to use freshly milled flour, but it does add nutrition and fiber. I purchased my Mockmill grain mill HERE. I buy all my wheat berries from Azure Standard.
3. Make browned butter for sourdough pumpkin cookies
In a small saucepan, melt the unsalted butter on medium heat. If you’d like to give the sourdough discard pumpkin cookies a nutty flavor, you can make it into brown butter by cooking it until it gets golden brown and begins to foam up. So, make sure to use a large enough saucepan because it tends to fuzz up and bubble over. Sadly, I did that today as I made these!! Regardless whether you use brown butter or just melted butter, they will be amazing.
4. Mix wet and dry ingredients
In the large mixing bowl, combine the wet ingredients, dry ingredients, and butter mixture (browned butter) with a wooden spoon, danish whisk, or hand mixer. I absolutely love my danish whisk because I don’t get a ton of cookie batter stuck in it. It’s perfect for brownies, cookies, pancakes, and batters that are a little thicker.
For best results, mix it until it is just combined so you don’t overwork the gluten in the flour and end up with tough cookies. You can also place the ingredients for the sourdough cookies in the bowl of a stand mixer and mix gently with the paddle attachment.
5. Add in chocolate chips
Once it’s just combined, add in the chocolate chips and gently mix in. For a rich flavor that’s not too sweet, my favorite thing to use is dark chocolate chips. So good!Â
6. Rest the batter
Preheat oven to 375 degrees. Cover with plastic wrap or a damp towel. Freshly milled wheat needs to rest so it can soak up all the moisture in the wet ingredients.
Let it sit for at least 15 minutes. Furthermore, this sourdough cookie batter can be put in the fridge for as much as 24 hours to allow the sourdough discard to begin to eat the sugar and gluten and make the sourdough pumpkin cookies more gut healthy.Â

7. Scoop the sourdough pumpkin cookies
After that, scoop small balls of cookie dough (I use a medium sized cookie scoop which gives me about 1 1/2-2 tablespoons of dough) onto prepared baking sheets. I use a cookie sheet lined with parchment paper. I can fit 24 cookie dough balls on a prepared baking sheet. A cookie scoop that is similar to what I use is HERE.
8. Bake
Bake cookies in a 375 degree oven for 10-12 minutes. I tend to take mine out at exactly 12 minutes for my oven. Play with the time to make sure you adjust it to your oven’s temperature.Â
9. Storing sourdough pumpkin chocolate chip cookies
Place the baked sourdough chocolate chip cookies to cool on a wire rack and serve immediately. Once they are cooled, take them off the cooling rack and store in an airtight container, Ziploc bag, or glass jar on the counter. Alternately, you may keep them in the freezer for longer storage.
***makes about 48 small cookies***
FAQs
Do I have to use fresh milled flour to make sourdough pumpkin cookies?
Although freshly milled flour adds nutritional density to these cookies, it’s not necessary. As a matter of fact, I made these with traditional all purpose flour for years before I started milling my own flour.
Can you freeze sourdough pumpkin cookies?
By all means, freeze these cookies! Due to the fact that I haven’t tried to use frozen cookie dough and bake them from frozen, I can’t recommend that. Normally, I bake them and then store in an airtight container with parchment paper between the layers of cookies. That works perfectly.
Above all, these little palm sized sourdough cookies that are full of pumpkin flavor and rich chocolate will be one of your favorite fall sourdough discard recipes! It’s such a perfect way to use leftover starter and create a cookie that is healthier and doesn’t make you feel guilty to eat it! So add this to your sourdough pumpkin recipe arsenal. All in all, you won’t be sorry.
Printable recipe card below:

Sourdough Pumpkin Cookies
Ingredients
Dry Ingredients
- Pinch salt
- 200g (1 cup) brown sugar
- 10g (2 teaspoons) baking powder
- 7g (1 teaspoon) baking soda
- 240g (2 cups) freshly milled soft white wheat, spelt or einkorn (you can also substitute all purpose flour and it works perfectly)
- 3g (1 teaspoon) cinnamon (for extra pumpkin pie flavor you can substitute pumpkin pie spice)
Wet Ingredients
- 1 room temperature egg
- 8g (1 teaspoon) vanilla extract
- 70g (1/4 cup) sourdough discard or active sourdough starter
- 1 small 15oz can of pumpkin puree (be very sure you are not using pumpkin pie filling)
- 1/2 stick unsalted butter, melted (can substitute a neutral tasting oil)
Add Ins
- 200-400g (1-2 cups) dark chocolate chips
Instructions
In the following recipe, I provide regular measurements, as well as scale weight. I think it's well worth it to purchase an inexpensive kitchen scale to make sure your baked goods have a consistency to them by always having the correct measurement of ingredients. However, I grew up in a measuring cup / teaspoon household so I've provided both.
1. Combine wet ingredients in a small bowl - room temperature egg, vanilla extract, sourdough starter discard, pumpkin puree.
2. In a large bowl, combine dry ingredients - salt, brown sugar, baking powder, baking soda, freshly milled flour (or all purpose flour), and cinnamon. NOTE: for a a change you can add pumpkin spice to add a depth of flavor and a taste of warm spices
3. In a small saucepan, melt the unsalted butter on medium heat. If you'd like to give the sourdough discard pumpkin cookies a nutty flavor, you can make it into brown butter by cooking it until it gets golden brown and begins to foam up. Make sure to use a large enough saucepan because it tends to fuzz up and bubble over. Sadly, I did that today as I made these!!
4. In the large mixing bowl, combine the wet ingredients, dry ingredients, and butter mixture (browned butter) with a wooden spoon, danish whisk, or hand mixer. Mix it until it is just combined so you don't overwork the gluten in the flour and end up with tough cookies. You can also place the ingredients for the sourdough cookies in the bowl of a stand mixer and mix gently with the paddle attachment.
5. Once it's just combined, add in the chocolate chips and just mix in. For a rich flavor that's not too sweet, use dark chocolate chips. So good!
6. Preheat oven to 375 degrees. Cover with plastic wrap or a damp towel. Freshly milled wheat needs to rest so it can soak up all the moisture in the wet ingredients. Let it sit for at least 15 minutes. However, this sourdough cookie batter can be put in the fridge for as much as 24 hours to allow the sourdough discard to begin to eat the sugar and gluten and make the sourdough pumpkin cookies more gut healthy.
7. Scoop small balls (I use a medium sized cookie scoop) onto prepared baking sheets. I use a cookie sheet lined with parchment paper. I can fit 24 cookie dough balls on a prepared baking sheet.
8. Bake cookies in a 375 degree oven for 12-14 minutes. I tend to take mine out at exactly 12 minutes for my oven.
9. Place the baked cookies to cool on a wire rack and serve immediately. Once they are cooled, take them off the cooling rack and store in an airtight container, ziplok bag, or glass jar on the counter. Alternately, you may keep them in the freezer for longer storage.
***makes about 48 small cookies***
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