How to Make Chocolate Chip Sourdough Cookies
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Sourdough chocolate chip cookies are the perfect guilt-free dessert! With a few tweaks, this recipes turns the classic cookie recipes into a nutrient dense, but still delicious cookie. Each cookie has a lower glycemic index, plenty of vitamins and nutrients, and that tangy sourdough flavor you know and love. We make these every week. I even keep a few batches of frozen dough ready to bake any time.
You are going to love these…
Sourdough Chocolate Chip Cookies with Fresh Milled Flour
Table of contents
- Sourdough Chocolate Chip Cookies with Fresh Milled Flour
- Why You’ll Love This Sourdough Cookie Recipe
- What Is Sourdough and why use it in cookies?
- Ingredients You’ll Need
- Equipment Needed
- How to Make Sourdough Chocolate Chip Cookies (Step-by-Step)
- How to Store Sourdough Cookie Dough or Cookies
- How to ServeYour Sourdough Cookies
- Most Common Questions about Sourdough Chocolate Chip Cookies
- More Sourdough Recipes You’ll Love
- Printable Recipe Card
- Leave a Comment and Share Your Results
Why You’ll Love This Sourdough Cookie Recipe
I know you will love this recipe, because we do! It is a regular dessert in our rotation. I try to keep all the ingredients on hadn’t so we can make a batch any time. If you keep a well stocked pantry, and especially if you store bulk grains for milling, you should have the ingredients on hand.
The coconut sugar lowers the glycemic index. And the combination of fresh milled flour with sourdough fermentation makes these cookies a powerhouse for nutrition. My kids and husband love these chocolate chip cookies. I’m confident yours will too!
What Makes This Recipe Different
This recipe is really the same basic ingredients as a traditional chocolate chip cookie. I’ve just made a few swaps to make it a little less sugary and little more healthy. I love using fresh milled flours to boost our nutrition, and this recipe is no different.
Coconut sugar is a great switch for lowering the glycemic index of a treat. It also lends that creamy caramel flavor to the recipe, which I love. You could use farm raised butter to really pack these cookies full of nutrients. Served with a glass of whole milk, it’s the perfect way to give your kids a treat that you can feel good about.
Who This Recipe Is Perfect For
Anyone! Who doesn’t love a chocolate chip cookie? With sourdough trending in the past few years, it’s not hard to get some starter. Whether you keep your own starter or need to borrow some from a friend, you should try this recipe soon!
What Is Sourdough and why use it in cookies?
I go much more in depth about sourdough starters in this article. And I discuss the health benefits of using the sourdough fermentation process. To sum it up, sourdough starter is a combination of flour and water that host live bacteria, yeast, and enzymes. Those enzymes break down anti-nutrients, help to digest carbohydrates, and give a natural lift to baked goods. Sourdough is more than just bread. It’s great for cookies, pancakes, bagels, and more!
A Brief History of the Chocolate Chip Cookie
Although chocolate had been incorporated into cookie dough earlier than the 1930s, it’s not well documented. The advent of chocolate chip cookies began in the 1920s when a late 19th century recipe of “jumbles”, a.k.a. drop cookies, found its way into the home kitchen. A woman tried making these drop style cookies with chunks of chocolate, rather than grating the chocolate into the dough. They were a hit.
Naturally, commercial kitchens and food factories got wind of the recipe. By the 1930s, chocolate chip cookies were widely available in grocery stores across the USA.
Why HomemadeCookies Are Better Than Store Bought
In a word: control. You get to control the ingredients (both the quality and the source). If organic is important to you, you’re the boss, so make organic cookies. Fermentation time is another reason to make your chocolate chip cookies at home. Even if you could spruce sourdough chocolate chip cookies from a store, it’s unlikely they’ll be long fermented.
hWhen you make cookies at home, you can decide then to be frugal. If you need to sub out an ingredient for something cheaper, you can! You can make substitutions, cater to your diet, avoid allergies, and do it all without going to the store.
Ingredients You’ll Need
Core Ingredients for Sourdough Chocolate Chip Cookies
- Fresh milled flour (my favorites for cookies are soft white wheat or spelt)
- Coconut sugar
- butter, melted
- salt
- baking powder
- baking soda
- dark chocolate chunks or chips
- white chocolate chips
- eggs
- Sourdough starter
Optional Add-Ins or Variations
If you don’t have any sourdough starter or discard, you can skip it. Since this recipe contains baking powder and baking soda, the cookies will rise without the fermentation process.
You can use brown sugar if you’re not looking for the health benefits of coconut sugar.
Use any combination of milk chocolate, semi-sweet chocolate, dark chocolate, white chocolate, or even peanut butter chips. Any shape is fine too. You can use chunks, chips, or whatever you have.
Equipment Needed
Essential Tools for making chocolate chip cookies
You can make this recipe very easily with a stand mixer and save yourself some work. But that’s not a requirement. I can manage this entire cookie recipe with the bare minimum:
- 2 bowls
- a whisk
- a spoon
- cookie sheet
- parchment paper
You’ll have to eyeball your measurements, use your finger to push the dough off the spoon, and possibly have inconsistent size cookies. And you’ll have to get your fresh milled flour from somewhere if you’re not milling it yourself. The benefits of fresh milled flour are worth the cost of a home grain mill. My favorite inexpensive grain mill is no longer on amazon, but I think this one is pretty similar.
Optional Tools That Make It Easier
SO, what I actually recommend using is a little bit longer list and few special tools to make it easier.
- cookie dough scoop
- silicone baking sheet instead of parchment paper
- sourdough whisk (or just use a stand mixer)
- grain mill for milling your spelt or wheat
How to Make Sourdough Chocolate Chip Cookies (Step-by-Step)
Step 1: Fresh Milled Flour
Mill your grains into flour. I like to use it immediately while it’s warm because it helps jump start the fermentation process.
Step 2: Measure ingredients
Measure out your ingredients carefully. Melt the butter.
Step 3: Combine Ingredients
- To melted butter, add the vanilla and coconut sugar. Mix well until fully combined. Stir in sourdough starter or discard.
- Then, add eggs. Whisk until thoroughly blended.
- In a separate bowl, whisk together the fresh milled flour, salt, baking powder, and baking soda.
- Combine wet ingredients with dry ingredients, being sure to coat all of the flour with the wet mixture.
Step 4: Add the Chocolate chips
Fold in your chocolate chunks or chips. To “fold in” mean to carefully slide your spoon or spatula under the dough, down the side of the bowl. Then, gently lift the spoon or spatula. Once you’ve lifted the dough on the spoon above the surface of the dough, flip your spoon so the dough folds over the top of the chocolate chips. Continue this motion until the chips are evenly distributed.
Step 5: Fermentation
Cover the bowl with a fabric bowl cover, plastic wrap, a wet tea towel, or a grocery bag. Let it sit at room temperature for 1-12 hours. If you want to long ferment, or if you’re nervous about leaving eggs out you can leave the bowl in the fridge overnight.
Step 6: Scoop the dough
Use a cookie scoop to scoop even amounts of cookie dough onto a baking tray or cookie sheet. Space them about 2-3 inches apart.
Strap 7: Bake or freeze
Bake at 375 for 10-12 minutes. Alternately, place the tray in the freezer until the balls of dough are hard. Transfer to a ziplock and freeze so you can pop them out anytime to bake.
Tips to help when you’re making Sourdough Chocolate Chip Cookies
- Melt your butter, even though most cookie recipes call for softened. Melted butter will soak into your fresh milled flour easily.
- Refrigerate dough before scooping.
- Preheat oven all the way.
- Serve warm with a glass of milk or coffee
Common Mistakes to Avoid with Fresh Milled Cookies
- Don’t mix yours eggs straight into hot melted butter.
- Whisk the baking powder, baking soda, and salt into the flour very well. Trust me, a bite full of baking powder is unpleasant.
- Make sure every single grain of flour is wet.
- Don’t stress about using fresh milled flour. trust the process.
- Don’t pay too much attention to the state of your starter.
Texture and Flavor Tips
These sourdough cookies will not be quite as sweet as traditional chocolate chip cookies due to the tang of the sourdough. Also, using coconut sugar gives more flavor but less sweetness. Use a milk chocolate chip if you need that extra sweetness while you get used to less sweet treats.
The texture will be slightly more gritty than regular cookies. Not like sand in your mouth, just different. Consider the germ and hull that have been ground up along with the flour form your whole grains. That extra texture is really just more nutrients and fiber. I am not saying this to put you off from trying the cookies- only to be realistic if you’ve never tried fresh milled flours.
My entire family loves and prefers fresh milled flour in all of our baked goods.
How to Store Sourdough Cookie Dough or Cookies
Refrigerator Storage
Keep the unbaked dough in the fridge for 3-5 days. Not only will it be convenient to bake a few cookies at a time, but also will continue to ferment. Baked cookies should last up to 2 weeks in the fridge.
Freezer Storage
Whether you bake them first, or freeze the raw dough, cookies will keep for 6 months in the freezer. Longer than that, and they may develop some freezer burn.
Shelf Life
These cookies should last a bout a week at room temperature. But really, they never last that long before being eaten. I keep mine on the counter in a cookie jar and we eat them all in a couple of days.
How to ServeYour Sourdough Cookies
- warm, with a glass of cold milk
- crumbled over ice cream
- with a hot cup of coffee
- as a grab and go snack
Most Common Questions about Sourdough Chocolate Chip Cookies
Yes! You just need this amazing Plain Living recipe and some time to let it ferment.
Definitely. In particular, soft white wheat or spelt make delicious cookies and brownies.
This flavor depends on ferment time. No matter what, they will have a bit of the sourdough tang. But like any sourdough product, the longer you let the dough ferment, the more acidic and sour it will become.
Absolutely, use discard in your cookies. The beauty of cookies is that you don’t have to fuss too much since the sourdough isn’t providing the rise.
Flat cookies usually come down to fat, flour, or temperature balance.
If your butter is too soft or melted, the cookies will spread before they set. Since we need to melt the butter to absorb into the flour, this dough will require a refrigeration period to solidify the butter again. Fresh milled flour can also affect this because it absorbs moisture differently than white flour. If your dough feels loose or sticky, it likely needs a bit more rest time.
Fresh milled flour creates a softer, more hearty cookie with a slightly nutty flavor.
Because the whole grain is used, including the bran and germ, the texture is a bit more rustic than cookies made with white flour. They may feel slightly thicker or more tender rather than light and airy.
The biggest difference is moisture. Fresh milled flour absorbs more liquid, so your dough may need a short rest before baking to fully hydrate. This helps avoid dry or crumbly cookies and gives you a better final texture.
You don’t have to—but it can really improve the cookies.
At a minimum, letting the dough rest for 30–60 minutes helps the flour fully absorb moisture. This is especially important when using fresh milled flour.
If you have more time, an overnight rest in the fridge allows a light fermentation to happen. This can deepen the flavor, improve digestion, and create a richer cookie without making it taste overly sour.
Short answer:
Quick bake: Rest 30–60 minutes
Better : Rest on counter for an hour, chill in fridge for 30 minutes. .
Best flavor: Chill overnight.
Both work well, but they give slightly different results.
Spelt flour tends to make a softer, more tender cookie with a mild flavor. It’s a great choice if you want something closer to a traditional chocolate chip cookie.
Fresh milled wheat (like soft white wheat) creates a heartier cookie with more structure and a slightly richer, whole grain taste.
If you’re just starting out, spelt is the easiest to work with. If you want more nutrition and a classic “from scratch” feel, wheat is a great option.
Soft and chewy cookies come down to a few simple adjustments.
Stick with the coconut sugar. Don’t swap it out for white or brown sugar. Be careful not to add too much flour since fresh milled flour is slow to absorb liquid. By the time it absorbs all the liquid, it will be too late because you thought you needed more.
Slightly underbake the cookies. They should look set on the edges but still soft in the center when you pull them out. They will continue to firm up as they cool.
Also, avoid overmixing the dough. Overmixing can create a more cake-like texture instead of that soft, chewy bite.
More Sourdough Recipes You’ll Love
Printable Recipe Card
Sourdough Fresh Milled Flour Chocolate Chip Cookies
Equipment
- 1 silpat optional
- 1 cooling rack optional
Ingredients
- 1 cup butter melted
- 1.5 cups coconut sugar
- 1 Tbs vanilla
- 2 eggs
- 4 cups fresh milled wheat flour
- 1 tsp baking soda
- 1 tsp baking powder
- 1 tsp salt
- 2 cups chocolate chips dark, milk, semi sweet, white, your choice
Instructions
Step 1: Fresh Milled Flour
- Mill your grains into flour. I like to use it immediately while it’s warm because it helps jump start the fermentation process.
Step 2: Measure ingredients
- Measure out your ingredients carefully. Melt the butter.
Step 3: Combine Ingredients
- To melted butter, add the vanilla and coconut sugar. Mix well until fully combined. Stir in sourdough starter or discard.
- Then, add eggs. Whisk until thoroughly blended.
- In a separate bowl, whisk together the fresh milled flour, salt, baking powder, and baking soda.
- Combine wet ingredients with dry ingredients, being sure to coat all of the flour with the wet mixture.
Step 4: Add the Chocolate chips
- Fold in your chocolate chunks or chips. To “fold in” mean to carefully slide your spoon or spatula under the dough, down the side of the bowl. Then, gently lift the spoon or spatula. Once you’ve lifted the dough on the spoon above the surface of the dough, flip your spoon so the dough folds over the top of the chocolate chips. Continue this motion until the chips are evenly distributed.
Step 5: Fermentation
- Cover the bowl with a fabric bowl cover, plastic wrap, a wet tea towel, or a grocery bag. Let it sit at room temperature for 1-12 hours. If you want to long ferment, or if you’re nervous about leaving eggs out you can leave the bowl in the fridge overnight.
Step 6: Scoop the dough
- Use a cookie scoop to scoop even amounts of cookie dough onto a baking tray or cookie sheet. Space them about 2-3 inches apart.
Strap 7: Bake or freeze
- Bake at 375 for 10-12 minutes. Alternately, place the tray in the freezer until the balls of dough are hard. Transfer to a ziplock and freeze so you can pop them out anytime to bake.
Notes
- Fresh Milled Flour Tip:
Fresh milled flour absorbs more moisture than store-bought flour. If your dough feels dry or crumbly, let it rest for 10–15 minutes before baking to fully hydrate. - Flour Options:
This recipe works well with fresh milled soft white wheat or spelt flour. Spelt creates a softer, more tender cookie, while wheat gives a slightly heartier texture. - Chilling the Dough:
For thicker cookies that don’t spread too much, chill the dough for 30–60 minutes before baking. This also improves flavor and texture. - Cookie Texture Tip:
For soft and chewy sourdough chocolate chip cookies, slightly underbake them. The centers should look soft when you remove them from the oven. - Prevent Flat Cookies:
If your cookies spread too much, your butter may be too warm. Chill the dough and make sure your baking sheet is not hot before placing dough on it. - Measuring Flour:
For best results, lightly spoon and level your fresh milled flour instead of packing it. Too much flour can make cookies dry or cakey. - Storage:
Store cookies in an airtight container at room temperature for up to a week. For longer storage, freeze baked cookies or dough balls for quick baking later. - Freezer Tip:
Freeze cookie dough in 2 tablespoon portions. Bake straight from frozen by adding 1–2 extra minutes to the baking time. - Flavor Variation Ideas:
Try adding chopped nuts, using dark chocolate chips, or sprinkling a little flaky salt on top before baking for extra flavor.
