Freshly Milled Sourdough Chocolate Chip Cookies
These refined sugar free and freshly milled sourdough chocolate chip cookies are soft, gooey, and packed with nutrients and chocolate chunks. Keep this recipe at the ready for a quick dessert or a long-fermented treat.

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This recipe is my go-to for an easy dessert. I recommend allowing this recipe to ferment overnight if you can. The fermentation makes the cookies healthier and adds a subtle tang that complements the sweetness. I highly suggest making the dough and only baking what you need. The dough will last in the fridge for a few days and your home will be filled with the delicious smell of fresh cookies. These freshly milled sourdough chocolate chip cookies are refined sugar free, which paired with the freshly milled flour won’t spike your blood sugar like traditional chocolate chip cookies.
If you don’t have access to a grain mill then you can use an alternative flour, like einkorn or kamut flour. This will aid in digestibility and add in extra nutrients compared to all purpose flour. It will also add depth to the flavor giving the cookies more of a nutty taste.
Using sourdough and fermenting your dough overnight will decrease the phytic acid and make the nutrients more bio-available and the grain more digestible – a win-win!

Why you’ll love freshly milled sourdough chocolate chip cookies
- Refined sugar free: This recipe uses maple syrup and your favorite chocolate chip to sweeten. The maple syrup is mineral rich. You can use milk chocolate, dark chocolate, semi-sweet, or date-sweetened chocolate chips.
- Freshly milled flour: Freshly milled flour is in its whole food form and packed with fiber, minerals, nutrients, and omega 3 fatty acids. Learn more about milling your own flour at home here.
- Use up your discard: This is a great way to use up your discard or use an active, bubbly starter.
- Versatile: Make this dough ahead of time and it can sit in your fridge for up to three days.
Ingredients
- Flour: With baked goods, I prefer to use about 2/3 freshly milled soft white wheat with 1/3 hulled barley. All purpose flour also works great.
- Butter: I use Mykonos dairy free butter, but this recipe works with any unsalted butter.
- Sourdough starter: Active starter or sourdough starter discard can be used.
- Vanilla extract: I use my homemade vanilla extract.
- Chocolate chips: I prefer mini chocolate chips, but dark or semi sweet of any size will be delicious.
- *Full ingredient list below
Tools you may need
Grain mill (optional)
Stand mixer (or hand mixer)
How to make freshly milled sourdough chocolate chip cookies
Step 1: In a stand mixer with a paddle attachment, cream together butter and maple syrup until blended. Add eggs, sourdough starter or sourdough discard, and vanilla. Mix again until light and fluffy.

Step 2: In a separate bowl, mill your flour (or use flour of choice), and mix with baking soda, baking powder, and salt.

Step 3: Slowly add dry ingredients to wet ingredients. Scrape down the sides and mix well.

Step 4: Add chocolate chips and mix well. Cover and chill the dough for at least an hour.

Step 5: Optional – If you would like to long-ferment the dough then cover the bowl or transfer to a sealed container. Place it in the fridge for 1-3 days.
Step 6: Preheat oven to 375°F.
Step 7: Roll cookies into a ball using three tablespoons of dough per cookie. Place them two inches apart of a parchment-lined baking sheet.

Step 7: Bake for 10-12 minutes until the edges start to turn golden brown.

Step 8: Remove from the oven and transfer to a wire rack to cool after two minutes.
Storage
Room temperature: Store in an airtight container at room temperature for up to a week.
Freezing baked cookies: Bake and allow to cool completely. Place the baking sheet in the freezer until cookies are frozen, then place cookies in an airtight container. Frozen cookies will last three months in the freezer. Allow to thaw at room temperature and then bake or toast for a few minutes to warm up.
Tips
- Ferment the dough for up to three days for the most health benefits or bake the cookies right away. I suggest putting the cookies in the fridge and baking a few every night over the three days.
- I recommend using mini chocolate chips.
- Be careful to not over bake your cookies. The cookies continue to cook on the sheet pan for a few minutes until transferred to a rack.
- Sourdough discard or active sourdough will work for this recipe since you do not need the dough to rise.


Freshly Milled Sourdough Chocolate Chip Cookies
Ingredients
Method
- In a stand mixer with a paddle attachment, cream together butter and maple syrup until blended. Add eggs, sourdough starter or sourdough discard, and vanilla. Mix again until light and fluffy.
- In a separate bowl, mill your flour (or use flour of choice), and mix with baking soda, baking powder, and salt.
- Slowly add dry ingredients to wet ingredients. Scrape down the sides and mix well.
- Add chocolate chips and mix well. Cover and chill the dough for at least an hour.
- Optional – If you would like to long-ferment the dough then cover the bowl or transfer to a sealed container and place it in the fridge for 1-3 days.
- Preheat oven to 375°F.
- Roll cookies into a ball using three tablespoons of dough per cookie. Place them two inches apart of a parchment-lined baking sheet.
- Bake for 10-12 minutes until the edges start to turn golden brown.
- Remove from the oven and transfer to a wire rack to cool after two minutes.
Notes
- Ferment the dough for up to three days for the most health benefits or bake the cookies right away. I suggest putting the cookies in the fridge and baking a few every night over the three days.
- I recommend using mini chocolate chips.
- Be careful to not over bake your cookies. The cookies continue to cook on the sheet pan for a few minutes until transferred to a rack.
- Sourdough discard or active sourdough will work for this recipe since you do not need the dough to rise.

