Fall-Spiced Sourdough Chocolate Chip Cookies with Spelt & Oats

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Fall Edition — A Year of Sourdough Chocolate Chip Cookies

Long-Fermented or No-Wait — Enjoy These Cozy, Fall-Spiced Sourdough Chocolate Chip Cookies with Fresh-Milled Spelt Flour, Hearty Oats & Sourdough Discard!

Closeup of half a spelt and oat sourdough chocolate chip cookie, resting on a black wire rack that's sitting o a patterned tea towel. Whole fall spices are visible at the side, next to a lightly grey, floral latte cup filled with foamy white milk. More chocolate chip cookies are cooling off in the background.
Cozy Up With A Warm Drink & Warm Spices
Closeup of half a spelt and oat sourdough chocolate chip cookie, resting on a black wire rack that's sitting o a patterned tea towel. Whole fall spices are visible at the side, next to a lightly grey, floral latte cup filled with foamy white milk. More chocolate chip cookies are cooling off in the background.
Cozy Up With A Warm Drink & Warm Spices

Fall is the kind of season that keeps you busy while luring you with the promise of coziness.
Checklists tend to run long, daylight increasingly short. There are so many things to be done (Preserve fall produce! Bake all the cozy things! Holiday season coming up!). And yet, nothing seems quite as promising as the thought of pulling on a pair of thick wool socks, putting up your legs and sipping a steaming cup of something, while watching dusk settle in earlier with each passing day.

These spelt and oat sourdough chocolate chip cookies are a lot like fall. They’re simple and quick to stir together, but you’ll have to wait a minute (or 48 hours) before you can slow down and enjoy a cookie break. It might just be best that way, too. After all, there’s usually a lot going on anyway, so splitting up the cookie making work is probably a blessing in disguise. Not a bad deal, right?

Why You’ll Love This Recipe

To me, sourdough has always been about flavor first. Fermentation naturally elevates flavors and if you combine it with freshly milled flour, you get to taste a richness that far surpasses a white flour, white sugar cookie. Depending on how tangy you like your cookies, you can let the cookie dough ferment in the fridge for up to three daysit’s up to you!

For an extra cozy fall treat, I added a rich blend of warming spices and wholesome oats for a little more toothsome texture. They’ll bake up like a classic chocolate chip cookiecrispy on the outside, tender on the inside.

You can ferment them now, and either bake right away or, in true make-ahead-fall-fashion, stash part of the rolled out cookie dough balls in the freezer for later. That way you’ll never be more than 20 minutes away from a fresh, delicious sourdough cookie in the future.

Spelt sourdough chocolate chip cookie dough rolled into balls, sitting on a lined baking tray.
Scooped and Ready to Bake.
Spelt sourdough chocolate chip cookie dough rolled into balls, sitting on a lined baking tray.
Scooped and Ready to Bake.

Tools You May Need

Wire Whisk and Silicone Spatula: These cookies can be made by hand, no appliances needed.

Bowl with a tight fitting lid (optional): Chill the dough in a bowl with a tight-fitting lid or wrap it really well to prevent the cookie dough from absorbing any unwanted fridge odors or flavors.

Cookie scoop (optional): Use a small cookie scoop for portioning out even amounts of fridge-cold dough. (I prefer these freshly milled sourdough cookies on the smaller side, as I find them notably more satisfying than their refined counterparts.)

Ingredients and Substitutions

Overhead shot of all ingredients for spelt and oat sourdough chocolate chip cookies.
Get Your Ducks In A Row

Whole Grain Spelt Flour Milling flour at home will give your cookies the best, complex aromas and also add a lot of nutrients. It’s the best feeling, walking away from a chocolate chip cookie (or two) and feel like you just had a balanced snack. If you’re not milling at home (yet), store-bought whole grain spelt flour will absolutely work in the meantime!

Sourdough Discard You can use active starter or discard less than 48 hours old for a milder sourdough flavor. Sourdough discard that’s been in the fridge for about a week is still active enough to ferment a batch of cookie dough. We’re not looking for rise, jut for flavor and the benefits of fermented grains.
New to Sourdough? You can learn how to grow your own starter and take good care of it in my Simple Sourdough Starter Series.

Rolled Oats Use old-fashioned rolled oats (not quick cooking or instant). They will soften during their time in the fridge, so smaller oats will just disappear into the batter.

Butter For dairy-free chocolate chip cookies, use a high quality vegan block butter (with a fat content of roughly 80% for the best texture in the finished cookies).

Chocolate Chips I use dark mini (i.e. regular German) chocolate chips and prefer them whenever I make smaller cookies. But really, all chocolate is welcome to cookies! Use your favorite chocolate chips, or any chocolate you have on hand. Chopping a whole chocolate bar is always an option as well.

Fall Spice Mix I put together my own mix of spices for a fall-festive flavor. If you don’t have all of the individual spices on hand, feel free to sub any missing (or polarising) spices with more cinnamon. You could also skip the mix altogether and use 4 teaspoons of your favorite pumpkin pie spice instead.

How to Make Sourdough Chocolate Chip Cookies with Freshly Milled Spelt & Oats

Closeup of sourdough discard being whisked into melted butter, slurred and ribboned.
A large heap of chocolate chips on top of spelt and oat sourdough cookie dough in a stainless steel bowl, resting on a striped tea towel.
Moody shot of spelt and oat sourdough chocolate chip cookie dough being scooped out of a stainless steel bowl.
Spelt sourdough chocolate chip cookie dough rolled into balls, sitting on a lined baking tray.

01

Prep and Combine Dry Ingredients

Weigh out whole spelt berries and grind them on the finest setting of your grain mill. Add baking powder, baking soda, spices and salt, and stir until well combined.

02

whisk together wet ingredients

In a medium large bowl, whisk together melted butter, sugar and brown sugar until well mixed. Add the sourdough discard and vanilla extract, and mix until combined. Add the egg and whisk just until fully incorporated.

03

mix in dry ingredients and add chocolate chips

Add the dry ingredients into the wet and stir until there are just a few streaks of flour left. Fold in oats until mostly incorporated, followed by the chocolate chips. Mix gently by hand until everything is just combined.

04

Cover and Ferment

Cover the bowl tightly and refrigerate for at least 2 and up to 72 hours, depending on how sweet or tangy you like your cookies.

05

Scoop and bake

Preheat the oven to 175°C (350°F). Use a cookie scoop to portion out even balls of cookie dough. Roll the dough into smooth balls between your palms and place them on a lined baking sheet.
Bake for 10-15 minutes, until the edges just turn golden brown. Let the cookies cool for one to two minutes on the baking sheet, before sliding the parchment paper onto a cooling rack, to cool completely.

Fresh milled spelt sourdough chocolate chip cookies on a black wire rack sitting on a patterned tea towel. Whole fall spices are scattered on the side, next tu a bright orange pumpkin and a cup of frothy milk tea.
Fresh milled spelt sourdough chocolate chip cookies on a black wire rack sitting on a patterned tea towel. Whole fall spices are scattered on the side, next tu a bright orange pumpkin and a cup of frothy milk tea.

Finding Your Perfect Fermentation Time

Sourdough cookie dough changes as it ferments in the fridge. The starter’s bacteria eat away at the sugars and starchesand that results in different cookies! Here’s an overview, to help you bake the kind of sourdough chocolate chip cookie you like best:

  • Texture: Cookies baked after just 24 hours in the fridge will have the crispiest outside and a soft centre. The longer they ferment, the more of the sugars get broken down, leading to a little less crisp on the outside. The oats will also soften over time, so the longer you wait, the softer they’ll be.
  • Sweetness: Spelt sourdough chocolate chip cookies baked after a day will still taste just as sweet as any regular cookie. You won’t really taste a difference in sweetness until the 48 hour mark. After 72 hours, they’ll be noticeably less sweet than a traditional cookie (which pairs nicely with the deeply complex fermented flavors.)
  • Tang: The longer you wait, the more of that signature sourdough flavor you’ll get. If you ferment for the full 72 hours, I find the sourdough even outbids the spices.

If you’re just getting into sourdough, I think you’ll enjoy these cookies most after 1 day of cold fermenting. They’ll taste like a regular chocolate chip cookie with a little something extra. For anyone used to sourdough flavors outside of a bread, 48 hours ist the sweet spot.

  • Make a Half-Batch: If a whole batch of cookies is more than you can go through within a week, you can only bake as many as you need and freeze the rest of the scooped and rolled cookie dough balls for another day. That way you can bake smaller batches whenever you crave fresh cookies. I’ve included instructions for freezing cookie dough here.
  • Don’t Overmix: For a crispy on the outside, chewy in the middle chocolate chip cookie, just stir in the egg and dry ingredients. If you prefer cakier cookies, use softened butter and cream it with the sugars until pale and fluffy.
  • Fold in Chocolate Evenly: Once the dough is firm, it’s impossible to redistribute the chocolate pieces, so make sure you fold the chocolate chips into the cookie dough evenly.
  • Label your Dough: Note the date and time on a sticky note or a piece of washi tape and stick it on the bowl or directly onto the wrapped dough. Sometimes you can get lost counting the days in the chaos of everyday life.
  • Shape Evenly: Use a small cookie scoop to portion out evenly sized cookies. For a more even, round shaped cookie, roll the scooped out dough into smooth balls between the palms of your hands.
  • Bake From Frozen: Freezing rolled cookie dough balls before baking results in the most uniform, “professional” shape, round and evenly domed.
Fresh milled spelt sourdough chocolate chip cookies on a black wire rack sitting on a patterned tea towel. Whole fall spices are scattered on the side.
Fresh milled spelt sourdough chocolate chip cookies on a black wire rack sitting on a patterned tea towel. Whole fall spices are scattered on the side.

How to Store and Freeze Sourdough Chocolate Chip Cookies

  • Storing Baked Cookies: Store cookies in a cookie tin (or other airtight container) at room temperature for up to 1 week (sometimes longer). Make sure they’re fully cooled before storing.
  • Freezing Baked Cookies: If you can’t go through the whole batch in time, place cooled cookies in a freezer-safe bag or airtight container. Remove as much air as possible to reduce freezer burn and ice crystal formation. Frozen cookies will keep for up to 3 months. To thaw, remove from the bag and let sit at room temperature overnight.
  • Freezing Cookie Dough (Highly Encouraged!): 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. Instant fresh cookies!

I’d love to hear how they turned out!

P.S. If you’re into sourdough chocolate chip cookies, check out the whole A Year Of Sourdough Chocolate Chip Cookies Series!


Fall-Spiced Sourdough Chocolate Chip Cookies with Spelt & Oats

These cozy sourdough discard cookies are made with fresh-milled spelt flour, rolled oats, and dark chocolate chips, warmly spiced with a homemade pumpkin spice blend. Perfect for fall baking, they’re chewy in the center, crisp on the edges, and naturally full of whole grain flavor. Ferment the dough anywhere from 2 to 72 hours to customize the sourdough tang, sweetness, and texture. A delicious way to use up sourdough starter discard — with an easy dairy-free option included!
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Fresh milled spelt sourdough chocolate chip cookies on a black wire rack sitting on a patterned tea towel. Whole fall spices are scattered on the side, next tu a bright orange pumpkin and a cup of frothy milk tea.
Prep Time:10 minutes
Cook Time:15 minutes
Fermentation Time:3 days
Total Time:3 days 25 minutes
Equipment
  • hand mixer - (Optional. Use only to stir on the lowest speed.)
  • wire whisk and silicone spatula - (These cookies can be made by hand, no appliances needed.)
  • Cookie Scoop - (Optional.)
  • cooling rack
  • kitchen scales
  • mixing bowl with a lid
Ingredients

dry ingredients

  • 260 g freshly milled spelt flour - (from 1⅓ cups whole spelt berries)
  • ½ tsp baking powder
  • ½ tsp baking soda
  • ½ tsp salt
  • 2 tsp ground cinnamon
  • ½ tsp ground mace
  • ½ tsp ground ginger
  • ½ tsp ground all-spice
  • ½ tsp ground cloves

wet ingredients

  • 225 g butter, melted - (1 cup/2 sticks) Use vegan block butter for dairy-free cookies.
  • 150 g sugar - (¾ cup) I use raw cane sugar
  • 100 g brown sugar
  • 120 g sourdough discard - or active starter
  • 1 large egg
  • 1 tsp vanilla extract

add-ins

  • 135 g old-fashioned rolled oats - (1½ cups)
  • 150 g chocolate chip cookies - (1 cup)
Instructions

Prep and Combine Dry Ingredients

  • Weigh out whole spelt berries and grind them on the finest setting of your grain mill. Add baking powder, baking soda, spices and salt, and stir until well combined.

Whisk Together Wet Ingredients

  • In a medium large bowl, whisk together melted butter, sugar and brown sugar until well mixed. Add the sourdough discard and vanilla extract, and mix until combined. Add the egg and whisk just until fully incorporated.

Mix in Dry Ingredients and Add Chocolate Chips

  • Add the dry ingredients into the wet and stir until there are just a few streaks of flour left. Fold in oats until mostly incorporated, followed by the chocolate chips. Mix gently by hand until everything is just combined.

Cover and Ferment

  • Cover the bowl tightly and refrigerate for at least 2 and up to 72 hours, depending on how sweet or tangy you like your cookies.

Scoop and Bake

  • Preheat the oven to 175°C (350°F). Use a cookie scoop to portion out even balls of cookie dough. Roll the dough into smooth balls between your palms and place them on a lined baking sheet.
  • Bake for 13-15 minutes, until the edges just turn golden brown. Let the cookies cool for one minutes on the baking sheet, before sliding the parchment paper onto a cooling rack, to cool completely.
Notes
  1. Chill the dough in a bowl with a tight-fitting lid or wrap it really well to prevent the cookie dough from absorbing any unwanted fridge odors or flavors.
  2. Ferment for 24 hours if you’re just getting into sourdough. They’ll taste like a regular chocolate chip cookie with a little something extra. For anyone well used to sourdough flavors, 48 hours ist the sweet spot.
  3. If you can’t go through a whole batch within a week, you can only bake as many as you need and freeze the rest of the scooped and rolled cookie dough balls for another day. Find instructions for freezing cookie dough here.
  4. For a crispy on the outside, chewy in the middle chocolate chip cookie, just stir in the egg and dry ingredients. If you prefer cakier cookies, use softened butter and cream it with the sugars until pale and fluffy.
  5. Note the date and time on a sticky note on the bowl or the wrapped dough. Sometimes you can get lost counting the days in the chaos of everyday life.
  6. Store cookies in a cookie tin (or other airtight container) at room temperature for up to 1 week (sometimes longer). Make sure they’re fully cooled before storing.
Servings: 35 small cookies
Calories: 115kcal
Author: Sarah | Grains & Greens Kitchen

Recipe FAQs

Absolutely! Use store-bought whole grain spelt flour instead of freshly milled.
If you’re in Europe, any regular whole wheat flour can be used as well.

I find that spelt and soft wheat can be used interchangeably in cookie recipes.
The distinction between hard and soft wheat is unique to North America, so if you’ve never come across hard wheat (other than on a bag of pasta), you’re probably baking in Europe or anywhere else in the world, where soft wheat is the only wheat available anyway.

If you don’t think you’ll enjoy your sour discard in a sweet cookie, either use fresh discard that’s less than 48 hours old, use active starter, or try my Sourdough Discard Reset Method!

Not at all! You can also bake these straight away once the cookie dough is chilled through. You’ll get more sourdough flavor and less sweetness, the longer you ferment in the fridge. Check out the post above to pick your perfect fermentation time.

Since the whole batch uses one whole egg, splitting the recipe is a little difficult. But I highly recommend freezing half a batch of dough when it has finished fermenting. Just roll it into balls, and freeze for later. You can bake the cookies directly from frozen! That way you can always make just as little or as many fresh cookies as you want.

Using your discard in recipes reduces waste. But it also adds depth of flavor and tang. I keep my starter the no-discard way, but I love feeding it extra from time to time, just to have some discard stashed away to add to other bakes.
Fermentation also helps with digestion by breaking down gluten and predigesting starches and sugars. If you want to read more about how to handle sourdough discard in your own kitchen, check out my What To Do With Sourdough Discard post.


Fresh milled spelt sourdough chocolate chip cookies on a black wire rack sitting on a patterned tea towel. Whole fall spices are scattered on the side, next tu a bright orange pumpkin and a cup of frothy milk tea.

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Recipe Rating




3 Comments

  1. 5 stars
    This is such a great recipe! I love all the spices in it and your instructions and explanations for fermenting these cookies are so super helpful. I must try these soon!

  2. 5 stars
    Since I could not find mace easily 🙄 I left it out. They were supposed to stay in the fridge for 48 hours, but ended up staying there for about 55. But they are great! Not too sweet, just the right amount of spice without it being overpowering. I will most definitely make these again! Even if mine didn’t turn out as pretty as yours😅 And with the whole grain flour I can even tell myself that they are practically healthy😂