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Home » Fresh Milled Flour Recipes

Fresh Milled Flour Sourdough Chocolate Chip Cookies

Published: Feb 24, 2025 by Parker · This post may contain affiliate links · 4 Comments

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As a mama who loves making food from scratch, I do my best to keep processed foods out of our home. Store-bought cookies are loaded with preservatives, artificial flavors, and questionable oils—not exactly what I want to be feeding my family. But while we all know fruits and veggies are the best choices, sometimes we need a real sweet treat, especially for special occasions. And this week, we have a big one—my daughter’s birthday!

Her favorite food? “Chockey chip cookies.” So, of course, I had to make her the best ones possible—homemade, using fresh-milled flour chocolate chip cookies as the ultimate way to celebrate. These cookies are soft in the middle, slightly crisp on the edges, and topped with flaky sea salt for the perfect balance of sweet and salty.  

4 fresh milled flour sourdough cookies stack on top of eachother vertically with a mason jar of milk in the background

Why You Will Fresh Milled Flour Sourdough Chocolate Chip Cookies

  • Made with fresh-milled flour– More nutrients, better flavor, and no processing!  
  • Naturally fermented – Thanks to the sourdough starter, they have improved digestibility.  
  • No artificial junk – Just simple, real ingredients.  
  • Freezer-friendly– Perfect for baking fresh cookies anytime.  

Equipment Needed:

  • Kitchen Aid Stand Mixer
  • Wooden spoon or spatula
  • Baking Sheet
  • Parchment paper
  • Measuring cups and spoons
  • Kitchen Scale
Ingredients for the Fresh Milled Flour Sourdough Chocoloate chip Cookies

Ingredients in Fresh Milled Flour Sourdough Chocolate Chip Cookies

  • 160g fresh-milled flour (100g soft white wheat, 60g kamut) – Fresh-milled flour keeps all the nutrients intact and gives the cookies a richer flavor. Soft white wheat creates a soft texture, while kamut adds depth and chewiness.  
  • 1 egg + 1 egg yolk (room temperature) – The egg provides structure, while the extra yolk makes the cookies extra rich and chewy.  
  • 1 stick butter (room temperature) – Butter adds flavor and creates that classic soft, slightly crisp cookie texture.  
  • 2 teaspoon vanilla extract – Enhances the sweetness and depth of flavor.  
  • ⅓ cup sourdough starter or discard – Adds moisture, complexity, and subtle tang, making these cookies even more flavorful and easier to digest.  
  • 66g sugar– Granulated sugar helps create the perfect balance of crisp edges and soft centers.  
  • 66g brown sugar – Brown sugar adds chewiness and a deeper caramel-like flavor.  
  • 1 teaspoon baking soda– Leavening agent that helps the cookies spread and rise slightly.  
  • 1 teaspoon salt– Balances sweetness and enhances flavor.  
  • 1.5 cups chocolate chip – Because chocolate is the heart of any fresh-milled flour chocolate chip cookie!  
  • Flaky sea salt (for topping) – Elevates the flavor by balancing the sweetness and adding a little crunch.  

If you love these Fresh Milled Flour Sourdough Cookies you May Also Like:

  • Refined Sugar Free Whip Cream
  • Fresh Milled Flour Sourdough Waffles

Instructions

Creamed sugars and butter

Cream butter and sugars

Cream the butter and sugars for 1-3 minutes until light and fluffy.  

Wet ingredients added to the butter and sugars and mixed together

Add in the wet ingredients

Add in the sourdough starter, vanilla, and egg + yolk, mixing until fully combined. 

Cookie dough mixed with the flours and the chocolate chips, ready to be shaped and refrigerated

Add the flours and Fold in the chocolate chips

Add the flour (stir setting on the kitchen aid) and then Fold in the chocolate chips to the dough. Roll the dough into 12 balls and refrigerate for at least 30 minutes (or overnight for better texture!).  

Chocolate Chip Cookies on a baking sheet

Shape the dough

Preheat oven to 375°F and line a baking sheet with parchment paper.  Place 6-8 cookies on the sheet (giving them room to spread).  Bake for 9-12 minutes (if they were chilled longer they will need more time, but check after 9 minutes for doneness).

.

4 fresh milled flour sourdough cookies stack on top of eachother vertically with a mason jar of milk in the background

Cool and enjoy!

Top with flaky sea salt when you pull them out of the oven. Let them rest on the cookie sheet for 5 minutes, and then transfer to a wire rack to cool. Then enjoy!

.

4 fresh milled flour sourdough cookies stack on top of eachother vertically with a mason jar of milk in the background

Fresh Milled Flour Sourdough Chocolate Chip Cookies

Parker
These Fresh-Milled Flour Sourdough Chocolate Chip Cookies are the perfect blend of chewy, rich, and lightly tangy flavors. Made with wholesome fresh-milled flour and packed with the health benefits of sourdough discard, they offer a delicious twist on a classic treat!
5 from 2 votes
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 4 minutes mins
Rest Time 25 minutes mins
Course Dessert, Fresh Milled Flour Recipes, Sourdough
Servings 8

Equipment

  • Kitchen Aid
  • Kitchen Scale
  • Measuring Spoons
  • Mixing Bowls
  • Grain Mill I love the nutrimill classic
  • Cookie Sheet
  • Parchment Paper
  • Cooling rack

Ingredients
  

  • 160 g fresh-milled flour 100g soft white wheat, 60g kamut- Kamut is non negotiatable, you will not get the same delicious flavor without it
  • 1 egg + 1 egg yolk room temperature
  • 1 stick butter room temperature
  • 2 teaspoon vanilla extract
  • ⅓ cup sourdough starter or discard
  • 66 g white granulated sugar
  • 66 g brown sugar
  • 1 teaspoon baking soda
  • 1 teaspoon salt
  • 1.5 cups chocolate chips
  • Flaky sea salt

Instructions
 

Cream Butter and Sugars

  • Cream the butter and sugars for 1-3 minutes until light and fluffy.

Add wet ingredients

  • Add in the sourdough starter, vanilla, and egg + yolk, mixing until fully combined.

Mix in the flours

  • Slowly mix in the fresh-milled flour, salt, and baking soda on low speed until just incorporated.

Mix in the chocolate chips

  • Fold in the chocolate chips.

Shape the dough and let it rest

  • Roll the dough into 12 balls and refrigerate for at least 30 minutes (or overnight for better texture!).

Preheat the oven and bake

  • Preheat oven to 375°F and line a baking sheet with parchment paper.
  • Place 6-8 cookies on the sheet (giving them room to spread).
  • Bake for 9-12 minutes, adjusting time based on how long they were chilled.

Top with flaky sea salt

  • Top with flaky sea salt as soon as they come out of the oven.

Cool and enjoy

  • Let cool for 3-5 minutes, then transfer to a wire rack.
Keyword Fresh Milled Flour Sourdough Chocolate Chip Cookie

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  • Why I Started Milling My Own Flour
  • Fresh Milled Flour Easter Blondies
  • Fresh Milled Flour Sourdough Cadbury Egg Cookies

Comments

  1. Hari says

    February 25, 2025 at 9:15 pm

    5 stars
    Such a delicious recipe! Love its final texture!

    Reply
    • Parker says

      February 27, 2025 at 10:08 pm

      Thank you, it's absolutely perfect if I do say so myself!

      Reply
  2. Jarrod says

    February 25, 2025 at 3:15 pm

    5 stars
    I'll try any chocolate chip cookie but you are going up against grandma! Thanks for sharing!

    Reply
    • Parker says

      February 27, 2025 at 10:08 pm

      ah I hope it measures up! Let me know how they turn out 🙂

      Reply

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Welcome! I’m so excited you’re here. Let’s roll up our sleeves and get cooking and baking from scratch to nourish our families with love and deliciousness. Can’t wait to share all the recipes with you!

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