Soft Sourdough Chocolate Chip Cookies Made with Fresh Milled Flour

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These are the easiest and softest homemade sourdough chocolate chip cookies you will ever make AND they are made with freshly milled flour! A twist on the classic cookie that’s more nutritious, more flavorful, and totally irresistible.

Whole wheat chocolate chip cookies are my go-to when I feel like baking, need to bring a snack to church, or have a play date. And it’s no wonder they’re such a staple; everyone loves a good fresh baked chocolate chip cookie. Add in the sourdough starter discard, and you’ve got some utterly delicious cookies.

These sourdough discard cookies are so delightful you won’t be able to eat just one!

Want more fresh milled recipes? Try making Fudgy Brownies, Lofthouse Copycat Cookies, or Molasses Cookies.

Benefits of Using Sourdough Discard in Cookies

If you haven’t noticed, I tend to add sourdough discard to most of my whole wheat cookie recipes. In my experience, it’s a great way to give my cookies more stability, a vitamin and mineral boost, plus more depth and flavor development.

Chilling your sourdough chocolate chip cookie dough overnight allows the fermentation process to happen, which gives you a bigger probiotic profile and makes your baked goods better for your body. Probiotics, like lactic acid bacteria, are non-pathogenic microbes that exert health benefits (Source). Yay for sourdough cookies!

Why Use Fresh Milled Flour?

Freshly milled flours retain all of the nutrients that processed flours often have removed or destroyed during commercial milling. “In fact, of the 44 known essential nutrients needed by our bodies and naturally obtained from foods, only 4 are missing from wheat– vitamin A, B_12, and C, and the mineral iodine.” – Sue Becker (Source)

Tools and Supplies

• Grain Mill
• Stand Mixer with Paddle Attachment/ Hand Mixer
• Spatula
• Cookie Sheet
• Silicone Baking Mat or Parchment Paper
• Cookie Scoop or Spoon
• Plastic Wrap

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Ingredients for the Sourdough Chocolate Chip Cookies

• 3/4 Cup Unsalted Butter, softened
• 1/3 Cup Sourdough Discard
• 1 Cup Brown Sugar
• 2 tsp Vanilla
• 1.25 Cups (250g) Soft White Wheat Berries
• 1 Egg
• 1 tsp Baking Soda
• 1/2 tsp Salt
• 1/2 tsp Cinnamon
• 1-1.5 Cups Chocolate Chips

Making Sourdough Discard Chocolate Chip Cookies

1. Add butter, sugar, and sourdough to mixing bowl and cream together
2. Mix in egg and vanilla
3. Mill flour and add to wet ingredients along with other dry ingredients
4. Mix dough until well combined
5. Add chocolate chips and mix until well dispersed
6. Cover bowl and refrigerate dough for 24 hours
7. When ready to bake, preheat oven to 350 degrees and line pan with mat
8. Using a medium cookie scoop, or large spoon, scoop dough and roll into cookie dough balls
9. Place dough balls onto mat or parchment-lined baking sheet and bake for 10-12 minutes, depending on size and oven
10. Let cool on pan for 1-2 minutes before moving to a cooling rack

Notes:

• I prefer to use mini chocolate chips or a mix of dark chocolate chunks and semi-sweet chips, but any milk chocolate or dark chocolate will work
• Chilling the dough is highly recommended, otherwise you may get flat cookies
• Don’t skip chill times for your dough – it allows fermentation to happen, the whole wheat flour to become fully hydrated, and it prevents the cookie from spreading too much when you bake them – it really makes a huge difference
• You don’t have to use an active sourdough starter, unfed discard works great
• Makes about 18 cookies, 3″ diameter 

Let’s Make Some Sourdough Discard Chocolate Chip Cookies

Chewy sourdough chocolate chip cookies aren’t just another mediocre recipe—they’re going to make you enjoy baking from scratch! By combining traditional techniques, whole grain ingredients, and a passion for fermented flavors, you’re not just baking cookies, but deliciously divine treats. Add in the secret ingredient of cinnamon and you’ll have your friends and family asking for more. 

You are going to fall in love with this sourdough chocolate chip cookie recipe! Fresh baked cookies will be on the menu tomorrow.

Storing Sourdough Chocolate Chip Cookies

These cookies don’t often last more than a couple of days in our house. Store cooled cookies in an airtight container on the counter for 3-4 days.

You can also freeze them easily. Once cooled, place cookies in a gallon bag and store in the freezer for 2-3 months. When ready to eat, you can let them thaw to room temperature or reheat in the microwave for 20-30 seconds.

Try Out Some Other Cookie Recipes:

• 
  Browned Butter Pumpkin Cake Cookies with Cream Cheese Icing
• 
  Sourdough Discard Molasses Cookie Recipe with Fresh Milled Flour
• 
  Sourdough Oatmeal Toffee Cookies: A Sweet and Chewy Treat

Or give our Snickerdoodles a go!

How Do I Mill Fresh Flour for My Cookies?

You’ll need a grain mill. They are an investment, but well worth it if you regularly bake bread, muffins, pancakes, etc. for your family. The basics are that you dump grain into a hopper that feeds it between stones to be ground and spit out into your bowl. Milling doesn’t take much longer than scooping flour from a bag.

I have a Mockmill which I love and would recommend to anyone, you can check out my review of the Mockmill.

Where Do I Buy Wheat Berries or Grain?

• Mockmill has a great variety to start you in your milling journey
• Azure Standard has great local pickups, so you don’t have to pay crazy shipping prices
• Central Milling is a great brand with lots of choices
• Country Life Foods (get 10% off your first purchase if you use this link)
• Pleasant Hill Grain is a great resource for everything milling-related
• Amazon even has a variety of wheat berries available
• King Arthur has some baking tools and appliances
• I often buy mine from a local Mennonite grocery store in 50-pound bags
• Check your local stores as many are starting to carry raw whole grains

Can I Just Use Store-Bought Whole Wheat Flour?

Of course! Choose a soft wheat variety. Hard wheat varieties have more gluten for bread that uses yeast to rise, while soft wheat is better for quick breads like muffins, or cookies.

Troubleshooting Common Cookie Baking Challenges

To prevent unwanted spread and to maintain shape be sure to chill your dough for at least 24 hours. You can also try swapping baking soda with baking powder or increasing your flour by 1/4-1/2 cup.

FAQS