Stuffed Sourdough S’mores Cookies (Gooey Center!)

If you are looking for the ultimate sourdough discard cookie, look no further. These Stuffed Sourdough S’mores Cookies are thick, gooey, and melting in the middle like a molten campfire treat! By using sourdough starter and extra egg yolks, I’ve achieved a dense, non-cakey crumb with the perfect balance of chew and crunch. Topped with dark chocolate chunks and graham cracker crumbles, these cookies offer a sophisticated depth of flavor that balances out the sweet, gooey marshmallow center. They require a quick chill, but one bite of that molten center will prove they are worth every second of the wait.

Essentials for the Perfect Sourdough Cookie

• Digital Kitchen Scale: In my kitchen, a digital scale is a non-negotiable! I have had this exact digital scale for years, and it has never failed me! Measuring by weight is the only foolproof way to ensure accuracy, especially for flour and sourdough starter which are often difficult to measure and can make or break the final texture of the cookies.
• Stand Mixer: A quality stand mixer is a game changer for sourdough cookies. It helps combine the thick dough with ease without over-mixing, which is key for a tender crumb!
• Large Cookie Scoop: Most of my sourdough cookie recipes are designed for making jumbo cookies. Using a large cookie scoop ensures that you get the bakery-style size with even baking every time!

Ingredients

• 3½ full graham cracker sheets, divided (55g): Using graham crackers on top and also in the dough helps to give these cookies that classic s’mores flavor!
• 8 large marshmallows: Large marshmallows are the key to the gooey molten marshmallow center! See important notes below about using homemade marshmallows.
• 1¼ cups light brown sugar, packed (275g): Make sure you pack it tight! The right amount of sugar gives the cookies the perfect amount of spread while keeping them chewy.
• 1 tbsp granulated sugar (13g): Including white sugar will help balance the moisture from the brown sugar, ensuring the cookies spread just the right amount.
• ½ cup salted butter, softened (113g): The perfect softness of the butter is “dent soft”, meaning it will indent somewhat easily when the corner is pressed with your finger, but still offers some resistance and is not completely room temperature yet. Let cold butter sit out for 30-60 minutes at room temperature. If you want to use unsalted butter, add ¼ tsp additional salt to the recipe.
• ½ cup sourdough starter, active or discard, stirred down (150g): The sourdough starter can be active or discard starter! Be sure to stir the starter down before measuring. Or for best accuracy, measure by weight.
• 2 large egg yolks (40g): Using just the yolks helps to give the cookies a gooey and chewy center rather than a cakey texture!
• 2 tsp vanilla extract (10g): Pure vanilla extract is best! Imitation vanilla often contains unnecessary additives.
• ½ tsp salt (3g): I prefer to use sea salt, as iodized salt may add an unwanted flavor profile.
• 1½ cups all-purpose flour, scooped directly from bag (not spooned or sifted) (235g): It’s very difficult to accurately measure flour by volume. This is because it is all dependent on how you scoop it! For ease of measuring, I designed this volume measurement to simply be scooped directly out of the bag (not spooned and leveled). Pro Tip: For the best accuracy and best overall cookie texture, you should measure flour by weight.
• 1 tsp baking soda (6g): Ensure you are using baking soda, NOT baking powder. They are not interchangeable and will affect the spread and texture of the cookie.
• 1 cup chocolate chunks (170g / 6 oz): For this recipe, I prefer dark chocolate chunks to balance the sweetness of the other ingredients! But you can use milk chocolate or semisweet chocolate chips if you prefer.
• 45 mini marshmallows: Using 3 mini marshmallows on top of each cookie is the perfect garnish! See notes below about swapping the large and mini marshmallows for homemade marshmallows to make what I call “ugly but worth it” cookies!

How to Make Stuffed Sourdough S’mores Cookies

Step 1: Preheat Oven & Prep

Preheat oven to 350°F (175°C). Line baking sheet with parchment paper.

Step 2: Prepare Graham Crackers & Marshmallows

Lightly crush 2 full sheets of graham crackers into crumbs and crumbles, then set aside. Break the remaining 1½ sheets of grahams into large chunks for topping the cookies, and set aside. Cut each large marshmallow in half, and set aside.

Step 3: Cream the Butter & Sugar

Start by beating the brown sugar, granulated sugar, and softened butter together. This works best with an electric mixer (either handheld or a stand mixer). You are looking for more than just a mix here, you want the texture to change, which takes about 3 minutes. It should look creamy, uniform, and slightly aerated. If you see chunks of butter, keep mixing!

Step 4: Add the Wet Ingredients

Add your sourdough starter, egg yolks, vanilla extract, and salt. Beat until it becomes smooth and slightly frothy. Tip: Make sure to scrape down the sides of the bowl with a spatula to ensure the starter is fully incorporated! You should not see any chunks floating around by this point.

Step 5: Incorporate the Dry Ingredients

Add your flour and sprinkle in the baking soda. Turn your mixer to low speed, and stir until just combined. Critical Step: Stop mixing when you still see a few tiny streaks of flour left. If you over-mix at this stage, you will accidentally over-develop the gluten and your cookies will be tough rather than soft and chewy.

Step 6: Fold in the Chocolate and Graham Crackers

Gently fold in the chocolate chunks and prepared graham cracker crumbles. Fold gently, preferably using a spatula, to ensure that they are evenly distributed without accidentally overworking the dough.

Step 7: Scoop & Stuff

Scoop dough into 15 equal portions using a large (3 tbsp / 70g) cookie scoop. Hollow out the center of each scoop with a spoon, and place a prepared half of a large marshmallow into the center of each well. Use your hands to gently seal the marshmallow inside the dough. Freeze for 30-45 minutes, or place in the fridge for at least 1 hour before baking. Note: You’ll have a half of a large marshmallow leftover that won’t be used in the recipe.

Step 8: Bake & Top

Place 6 dough balls onto the prepared baking sheet, ensuring even spacing. Bake for 10 minutes. Remove from the oven, rotate the pan, and quickly top each partially baked cookie with 3 mini marshmallows, the prepared chunks of graham cracker for garnish, and optionally a few additional chocolate chunks. Bake for an additional 5-7 minutes. You’ll know they’re done when edges are slightly crisp, though the center will remain soft since it’s a stuffed cookie. Bake in batches until all cookies are finished.

Step 9: Cool On Baking Sheet

Let the cookies sit on the hot baking sheet for right around 7 minutes before transferring them to a cooling rack. This is a crucial step for ensuring that the cookies set up completely. If you try to move them too soon, they will fall apart.

How to Store:

Once completely cool, you can store cookies in an airtight container or bag for up to 5 days at room temperature.

Frequently Asked Questions

Can I use homemade marshmallows?

Homemade marshmallows, especially my vanilla bean marshmallow recipe, always taste better than store-bought options in my opinion! However, because homemade gelatin marshmallows have a high water content and no strong stabilizers, they do not withstand oven temperatures and will melt completely in the oven. Sometimes though, I use homemade marshmallows to get a better flavor, and I call them “ugly but worth it” cookies (image above!). They are not a uniform shape and always melt and caramelize completely all over the pan in a puddle, but the flavor is simply unbeatable!

Can I toast the marshmallows?

Absolutely! Use a kitchen torch to lightly toast marshmallows after baking for an even toastier flavor. Note: If you really want to use homemade marshmallows and still have pretty cookies, then skip the stuffed step entirely, bake cookies completely before topping with homemade marshmallows, and then use the kitchen torch to toast them lightly.

Will these cookies taste sour?

If you skip the long-fermentation, then these cookies will not taste sour at all. The sourdough starter provides a beautiful depth of flavor that balances the sweetness of the chocolate and marshmallows, but it does not make the cookies taste like a loaf of sourdough bread. The longer you ferment the dough in the fridge however, the more developed the sourdough flavor will be.

How do I get the center gooey again after the cookies have cooled?

While these cookies are delicious at room temperature, that signature molten marshmallow center is best when warm! To get that freshly-baked experience again, simply pop a cookie in the microwave for 8–10 seconds. This softens the marshmallow center and the chocolate chunks back to ooey gooey perfection!

Can I freeze sourdough cookie dough?

Absolutely! For best results, follow this flash-freezing method:

1. Scoop & Stuff: Follow the directions exactly as described for making all of the stuffed cookie dough balls, including placing them into the freezer.
2. Flash Freeze: Freeze for about 1 hour, or until the dough balls are firm to the touch.
3. Store: Transfer the frozen dough balls into a gallon freezer bag. They can be stored in the freezer for up to 3 months!

Pro Tip: Double the recipe to intentionally freeze an extra batch! This provides you with ready-to-bake sourdough s’mores cookies for when that sweet tooth hits.

Tips For Baking Frozen Dough:

You may need to add 1–3 minutes to the baking time if the dough balls are frozen solid.

How to Make Long-Fermented Stuffed Sourdough S’mores Cookies

To long-ferment the dough for more flavor, gut health, and nutritional benefits, follow these simple directions:

1. Prepare: Follow the recipe directions to make the dough.
2. Cold Ferment: Cover the bowl with plastic wrap, or transfer to an airtight container. Refrigerate for 1–3 days. Note: After the first day, longer fermentation increases the health benefits, but it also intensifies the tangy flavor.
3. Bring to Room Temp: Remove the dough from the fridge and allow to sit at room temperature for about 1 hour before continuing on with the stuffing steps. Cold dough is too stiff to scoop.
4. Scoop, Stuff, Freeze, & Bake: Once dough has come to almost room temperature, scoop (3 tbsp / 70g each) and stuff with marshmallow as listed in the directions. Critical Step: As per the directions, you still need to do the 30-45 minute freeze after the scoops have been stuffed before baking!
   

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