Bakery-Style Sourdough Discard Chocolate Chip Cookies

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Sourdough discard chocolate chip cookies that are soft, bakery-style, and chocolate-studded—with a long-fermented option for deeper flavor.

A plate of sourdough discard chocolate chip cookies and strawberries on a table.
Long-fermented sourdough chocolate chip cookies and a generous handful of strawberries—the perfect summertime snack combination.
Long-fermented sourdough chocolate chip cookies and a generous handful of strawberries—the perfect summertime snack combination.

These sourdough discard cookies have been a longtime favorite in my kitchen—a slightly more nourishing, low-effort twist on the classic chocolate chip cookie I adore. They were born during my first pregnancy, when I had an unstoppable 10:30 a.m. cookie craving every single day, without fail. If I was going to build a baby on cookies, I figured they should at least offer something a little better.

Using sourdough discard instead of bubbly starter makes this recipe extra practical (and zero waste!). The long, slow ferment adds a gentle tang and depth of flavor that sets these apart from your everyday chocolate chip. I always use vanilla sugar in place of extract—a little nod to my German kitchen roots—which gives the cookies a warm, familiar aroma that feels like sunshine in every bite.

Whether you’re baking with classic all-purpose flour or freshly milled soft wheat, this cookie dough comes together easily and only gets better after a few days of resting in the fridge. Perfect for a summer afternoon—tender, chocolatey, and just the right amount of tang—these cookies have been my go-to indulgence for years, and I hope they’ll become yours, too.

P.S.: They’re still my go-to for 10:30.

Why This is My All-Time Favorite Sourdough Discard Chocolate Chip Cookie Recipe

Rest assured: if I’m asking you to wait three days before you get your hands on a chocolate chip cookie, I made double sure that you walk away with a truly awesome cookie experience. Slow cold fermentation delivers a deeply flavorful, tangy cookie. Semi-sweet chocolate comes in both chunks and tiny flecks, for extra texture. Plus: you get to decide how sweet or tangy you want them to be. The longer they ferment in the fridge, the more time the bacteria in your starter have to consume the sugar and develop flavor — it’s up to you!

That, the added health benefits of sourdough fermentation, and the tender and cakey, bakery-style texture make these a treat to remember. High impact on your taste buds — low impact on your gut!

A hand holding a sourdough chocolate chip cookie with fresh strawberry in the background.

Tools You May Need

Stand mixer or hand mixer: For creaming butter, sugar and eggs.

Bowl with a tight fitting lid (optional): A tight lid will keep out unwanted flavors during the 3-day cold ferment.

Cookie scoop (optional): For portioning out even amounts of fridge cold dough.

Ingredient Notes and Substitutions

  • All-purpose flour: I use German all-purpose flour, but in all my years of baking from standard American cookie recipes I have never had any hiccups. So I feel confident in recommending you use any all-purpose or plain flour available to you.
  • Vanilla sugar: I use vanilla sugar for a warm aroma and tiny black flecks throughout the batter (it’s easily made at home if needed). You can use vanilla extract instead, if it’s more available to you, or just rub the seeds from half a vanilla bean into the sugar before whipping up the batter.
  • Sourdough discard: Discard that spent less than a week in the fridge is still active enough to perfectly ferment a sourdough cookie! We’re not looking for rise but for flavor and gut healthy fermentation.
  • Chopped semi-sweet chocolate: I’m a chocolate purist at heart, so semi-sweet (or even darker) is my go to. A good quality chocolate chip is a convenient shortcut though – and one I’m more than willing to take if needed.

My Favorite Sourdough Discard Chocolate Chip Cookie Recipe (Step-by-Step)

A bowl of vanilla flecked sourdough chocolate chip cookie dough.
A bowl of golden sourdough discard cookie dough with a large amount of chopped dark chocolate on top.
Scoops of chocolate studded cookie dough balls on a parchment lined baking tray in bright sunlight.

01

Combine dry ingredients

In a medium bowl, combine flour, baking powder, baking soda and salt. Stir until well combined.

02

Cream butter and sugar

In a medium large bowl or the bowl of a stand mixer, cream butter, sugar, brown sugar and vanilla sugar until pale and fluffy (around 2 minutes).

03

Add sourdough discard and egg

Add the sourdough discard and mix until combined. Add the egg and beat on low until fully incorporated.

04

Mix and add chopped chocolate

Slowly add the dry ingredients to the wet and mix on low until well combined. Add the chopped chocolate and mix until just incorporated (or fold them in by hand).

05

Cold-ferment for one to three days

Cover the bowl tightly and refrigerate for one to three days, depending on how sweet or tangy you like your cookies.

06

Scoop and bake

Preheat the oven to 175°C (350°F). Use a cookie scoop to portion out even balls of cookie dough. Place them on a lined baking sheet and press the dough balls flat ust a little, so that they don’t have a dome on top. Bake for 14-18 minutes, just until the edges turn golden brown. Wait until thoroughly cooled before removing them from the parchment paper.

Sourdough discard chocolate chip cookies with melted chocolate chunks and golden brown edges cooling off on a parchment lined cooling rack.

Tips

  • For cookies with a cakier texture, beat the egg into the creamed butter and sugar until the mixture is pale and fluffy. For a flatter, crispier cookie, add the egg and mix just until well combined.
  • Mix chopped chocolate evenly into the dough before refrigerating. Once the dough is firm, it’s impossible to redistribute the chocolate pieces.
  • Chill the dough in a bowl with a tight-fitting lid or wrap it really well to prevent it from absorbing any unwanted fridge odors or flavors.
  • Use a cookie scoop to portion out evenly sized cookies for uniform baking. If you don’t have a scoop at hand, try something similar – like a coffee scoop. Any kind of deep spoon that can be leveled off will do nicely!

Variations

  • Whole wheat cookies: Use whole wheat flour for an extra healthy treat. For best taste, maximum nutrition (and baby growing fuel) use freshly milled soft wheat flour. The texture will be a bit denser but still delicious. If the dough feels too stiff, add 1–2 tablespoons more sourdough discard.
  • Sweeter cookies: During the cold ferment, the starter’s bacteria consume the sugars in the dough. After 3 days, they’re less sweet than traditional versions. If you want them sweeter, bake after 24-48 hours of fermentation.
  • Less tang: For a milder sourdough flavor, use active starter or discard that’s less than 24 hours old. The longer they ferment, the deeper and tangier the flavor.
A blue bowl of golden Sourdough discard chocolate chip cookies sitting on a blueberry-patterned linen tea towel in golden sunlight.
Sourdough discard chocolate chip cookies with melted chocolate chunks and golden brown edges served on a blue plate.

How to Store and Freeze Chocolate Chip Cookies

  • Storing Baked Cookies: Store cookies in an airtight container or cookie tin at room temperature for up to 1 week. Make sure they’re fully cooled before storing to maintain texture and prevent moisture buildup.
  • Freezing Baked Cookies: Let cookies cool completely, then place them in a freezer-safe bag or airtight container. Press out as much air as possible to reduce freezer burn and ice crystal formation. Frozen cookies will keep well for up to 3 months. To thaw, remove from the bag and let sit at room temperature overnight.
  • Freezing Cookie Dough (Highly Recommended): Portion out the dough into balls, place on a baking sheet, and freeze until solid. Transfer to a freezer-safe bag, removing excess air. Bake directly from frozen—no need to thaw. Just add 2–5 minutes to your usual baking time.

I’d love to hear how they turned out!

P.S. If you’re into tangy sourdough cookies, you might want to check out the whole A Year of Chocolate Chip Cookies Series!


Bakery-Style Sourdough Discard Chocolate Chip Cookies (Long-Fermented Option)

Tender, nostalgic bakery-style sourdough discard cookies—rich with dark chocolate, infused with vanilla, and a gentle tang from long fermentation. Melt-in-your-mouth soft, cakey, and golden at the edges. Big flavor, low gut impact.
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Sourdough discard chocolate chip cookies with melted chocolate chunks and golden brown edges served on a blue plate.
Prep Time:10 minutes
Cook Time:30 minutes
Fermentation Time:3 days
Total Time:3 days 40 minutes
Equipment
  • Stand Mixer or Hand Mixer
  • Cookie Scoop - (optional)
Ingredients
  • 225 g butter - 1 cup
  • 150 g raw cane or plain sugar - ¾ cup
  • 100 g brown sugar - ½ cup
  • 1 ½ tsp vanilla sugar - or 2 tsp. vanilla extract
  • 120 g cup sourdough discard - ½ cup
  • 1 large egg
  • 345 g all-purpose flour - 2⅔ cup
  • ½ tsp. baking powder
  • ½ tsp. baking soda
  • ½ tsp. fine salt
  • 100-150 g chopped dark chocolate - ¾ – 1 cup (I used 100g / ¾ cup)
Instructions
  • In a medium bowl, whisk together the flour, baking powder, baking soda, and salt until well combined.
  • In a separate large bowl, cream the butter with the sugars until the mixture is light and fluffy. Add the sourdough discard to the butter mixture and mix until incorporated, then beat in the egg until fully combined (see Notes for texture variations).
  • Add the dry ingredients to the wet, mixing on low speed until just combined. Fold in the chopped chocolate pieces.
  • Cover the dough tightly and refrigerate for 1 to 3 days, depending on how tangy and developed you want the flavor.
  • When ready, preheat the oven to 175°C (350°F). Scoop even portions of dough onto a lined baking sheet, gently flattening each ball. Bake for 14 to 18 minutes, until the edges are golden brown. Allow cookies to cool completely before removing from the baking paper.
Notes
Tips
  • For a cakier cookie, beat the egg into the butter and sugar until the mixture is light and fluffy. If you prefer a thinner, crispier cookie, just mix the egg in until combined—no extra beating needed.
  • Make sure to mix the chopped chocolate evenly into the dough before chilling, since once it’s cold, the chocolate pieces won’t move around much.
  • Store the dough in a bowl with a tight-fitting lid or wrap it well to keep fridge odors out during the long rest.
  • Using a cookie scoop helps portion the dough evenly so your cookies bake uniformly. No scoop? A level coffee scoop or spoon works just fine, too!
Variations
  • Whole Wheat Cookies: Swap in whole wheat flour for a nuttier, more nutritious cookie. Freshly milled soft wheat flour works beautifully here, though the dough may feel a bit stiffer — if so, add an extra tablespoon or two of sourdough discard to loosen it up.
  • Sweeter Cookies: Since fermentation eats up some of the sugar, cookies fermented for 3 days taste less sweet than usual. If you want them sweeter, try baking the dough after 1 or 2 days instead.
  • Less Tang: To keep the sourdough flavor mild, use fresher discard (less than 24 hours old) or even active starter. The longer you ferment, the tangier the cookies get, so feel free to experiment!
Servings: 24
Calories: 203kcal
Author: Sarah | Grains & Greens Kitchen

Recipe FAQs

Yes! Active starter will work, especially for shorter ferment times. It won’t be quite as tangy, but it’ll still add depth. If you’re brand new to sourdough, check out my Simple Sourdough Starter Series.

Anywhere from 1 to 3 days in the fridge. The longer the rest, the tangier and less sweet the cookies will be. I personally go all-in with a 3-day ferment for the most intense flavor but if you’re fairly new to sourdough, consider starting with 2 days and see how you like it!

No — any plain or all-purpose flour will work just fine. But if you’re curious about the hows and whys of home milling, I’ve shared more in my post on Milling Flour at Home.

Absolutely. Chocolate chip cookies freeze beautifully, both raw and baked. Check the full post for freezing tips!

Besides reducing waste, sourdough discard adds depth of flavor and a gentle tang. Plus, fermentation helps with digestion by breaking down gluten and predigesting starches and sugars. Learn more about sourdough discard in my What To Do With Sourdough Discard post.

Yes, absolutely! The structure of your discard may have collapsed, but the bacteria inside is still alive and hungry! They will start consuming the flour and sugar in the cookie dough, regardless. If you’re worried about the performance of your discard, you can give the dough a small fermentation head start: just leave it on the counter for an hour or two before you move it to the fridge.

Bakery-style cookies are thicker and cakier in texture. They’re tender-crumbed and not snappy. Classic American Chocolate Chip cookies are usually crispy on the edges and chewy in the middle. Check out the Tips section above to learn how to achieve both textures with this recipe.


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Recipe Rating




4 Comments

  1. 5 stars
    You got my attention with this recipe! Love everything about it and can’t wait to try it. Great ingredients and easy to follow instructions too! Awesome!❤️

  2. 5 stars
    I used vegan butter because baking on a Sunday comes with restrictions 😅 otherwise I followed the recipe, using freshly milled flour, and left them in the fridge for two days. I tested them on various people and they were a success! People tasted a difference but nobody could pinpoint what the secret ingredient was. They were however uniformly of the opinion that these are good cookies 😊 So, another great recipe for using up discard (I actually fed my discard to have enough for this recipe…)

    1. That’s the kind of kitchen ingenuity we’re here for 👏🏻😋
      I’m glad people loved them (they never last long around here either)!
      Whenever I feed my starter these days, I feed it a little extra extra. You never know what’ll come up and if I don’t get to use it elsewhere.. well, there’s always cookies! 😀