Chocolate-stuffed sourdough peanut butter cookies are soft, chewy peanut butter cookies with a rich chocolate ganache center that melts in every bite. They're the perfect balance of salty, sweet, and fudgy — and the sourdough discard adds a subtle tang that deepens the flavor while keeping the cookies soft for days.
These are indulgent, bakery-style cookies you'll want to make again and again. If you love them, try my sourdough peanut butter blossom cookies for another soft, chewy sourdough treat — or my classic sourdough peanut butter cookies if you're after a simple, fool-proof staple.
Quick Look: Chocolate-Stuffed Sourdough Peanut Butter Cookies
⏱️ Ready In: about 42 minutes (plus 1–2 hours to chill the ganache)
🔥 Bake Time: 10–12 minutes
🍽️ Serves: 24 cookies
✨ Calories: 266 per cookie
🥄 Main Ingredients: peanut butter, sourdough discard, chocolate ganache, brown sugar
🌿 Dietary: Vegetarian
💛 Why You'll Love It: soft peanut butter cookies with a gooey chocolate ganache center
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Why You'll Love This Recipe
A molten ganache center. Each cookie hides a scoop of rich chocolate ganache that stays gooey and melty after baking. If you love chocolate the way I do, you need to try my sourdough chocolate muffins immediately!
Salty-sweet perfection. Creamy peanut butter and a roll in sugar against a fudgy chocolate center hit every craving at once.
Tangy, soft sourdough. The discard adds a subtle tang and keeps these soft for days, while using up your starter.
Bakery-style cookies at home. Big, thick, and impressive — perfect for gifting, just like my sourdough chocolate peanut butter swirl cookies.
No dough chilling needed. Only the ganache chills, so the cookie dough comes together and bakes right away.
Jump to:
- Quick Look: Chocolate-Stuffed Sourdough Peanut Butter Cookies
- Why You'll Love This Recipe
- Ingredients You'll Need
- Easy Substitutions & Variations
- How to Make Chocolate-Stuffed Sourdough Peanut Butter Cookies
- Expert Tips
- What Makes This Recipe Special?
- Chocolate Stuffed Cookie Cookie FAQs
- Stuffed Cookie Troubleshooting Guide
- Storage
- Other Sourdough Recipes to Consider
- Chocolate Stuffed Sourdough Peanut Butter Cookies
Ingredients You'll Need
For the chocolate ganache filling:
- Semi-sweet or bittersweet chocolate chips — the molten center.
- Heavy cream — to melt the chocolate into a smooth ganache.
- Unsalted butter — for shine and a silky texture.
For the cookie dough:
- Unsalted butter — softened and creamed for a soft base.
- Brown and white sugar — brown for chew, white for structure (plus more for rolling).
- Vanilla extract — rounds out the flavor.
- Egg and egg yolk — the extra yolk adds richness and chew.
- Sourdough discard — adds a subtle tang and keeps the cookies soft.
- Creamy peanut butter — for that classic salty-sweet flavor.
- All-purpose flour, baking soda, and fine sea salt — the base and lift.
- Instant espresso powder (optional) — deepens the chocolate flavor.
Easy Substitutions & Variations
Nut butter swap: Creamy almond or cashew butter works for a different nutty flavor.
Ganache shortcut: Use store-bought truffles or chocolate caramels instead of homemade ganache.
Gluten-free: A 1:1 gluten-free flour blend works, though the cookies may spread slightly more.
Nutty crunch: Roll the dough in crushed peanuts before baking for extra texture.
Milk or dark chocolate: Swap the semi-sweet ganache for milk or dark chocolate to suit your taste — or, for an all-chocolate fix, try my easy double chocolate filled cookies.
Build a cookie box: Pair these with my brownie crumb bars, sourdough oatmeal cookies, and my gingerbread latte cookies for a chocolate-and-peanut-butter dessert spread.
How to Make Chocolate-Stuffed Sourdough Peanut Butter Cookies
Note: I bake by weight for accuracy. Cup measurements are approximate and may vary depending on how you scoop.
Step 1: Ganache: Make and chill in the refrigerator ganache until scoopable.
Step 2: Dough: Cream butter + sugars, then mix in wet and dry ingredients.
The picture above shows a double batch.
Step 3: Assemble: Scoop, flatten, stuff with ganache, seal, and roll in sugar.
Step 4: Bake: 10-12 minutes at 350°F. Cool 5 minutes before transferring.
Weigh your ingredients! Using a kitchen scale ensures your measurements are accurate, which is key for getting consistent results in baking. It takes the guesswork out of measuring and helps your recipes turn out exactly as intended every time.
Expert Tips
1. Chill the ganache until firm. It must be scoopable and solid to stuff easily — and it'll stay perfectly melty after baking. This is the key step.
2. Seal the dough well. Wrap the dough fully around the ganache with no gaps, so the chocolate doesn't leak out while baking.
3. These don't spread much. Press them down with a fork before baking, since they hold their shape rather than flattening on their own.
4. Pull them soft. Take them out when the edges are set but the centers still look soft — they finish setting on the pan.
5. Scoot for round cookies. Swirl a large round cookie cutter around each warm cookie for bakery-perfect edges.
What Makes This Recipe Special?
Peanut butter and chocolate is a classic pairing, but stuffing these cookies with a true chocolate ganache (rather than just adding chips) takes them somewhere special. Bite in and the center is genuinely molten — a rich, fudgy pocket against the soft, salty-sweet peanut butter dough. The sourdough discard does quiet work in the background, adding a subtle tang that balances the sweetness and keeps the cookies tender for days.
The result is an indulgent, bakery-style cookie that looks and tastes far more impressive than the effort required. It's the same crowd-pleasing peanut-butter-and-chocolate magic as my classic sourdough peanut butter cookies, dialed all the way up.
Chocolate Stuffed Cookie Cookie FAQs
Yes, make it up to a few days ahead and keep it chilled. You can even pre-scoop the ganache balls and freeze them for easy stuffing.
The dough wasn't fully sealed, or the ganache was too soft. Make sure it's firm and wrap the dough completely around it.
Yes, fed or unfed both work, since the discard is for flavor and texture rather than rise.
No, they hold their shape, so press them down with a fork before baking.
Stuffed Cookie Troubleshooting Guide
| Problem | Cause | Fix |
|---|---|---|
| Ganache leaked out | Dough not sealed, or ganache too soft | Chill ganache firm; seal dough fully |
| Cookies stayed too round | They don't spread much | Press down with a fork before baking |
| Dry cookies | Overbaked | Pull when edges are set but centers soft |
| Ganache not scoopable | Not chilled enough | Refrigerate 1–2 hours until firm |
| Dough too sticky to wrap | Peanut butter too soft/oily | Use a no-stir creamy peanut butter |
Storage
Room temperature: Store in an airtight container for 3–5 days.
Refrigerator: Keeps up to 1 week.
Freezer: Freeze baked cookies for up to 6 months. Warm slightly before eating for gooey centers.
Other Sourdough Recipes to Consider
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Chocolate Stuffed Sourdough Peanut Butter Cookies
Equipment
- Kitchen Scale
- Stand Mixer
- Measuring spoons
- Heatproof bowl (for ganache)
- Small saucepan (for heating cream)
- Spatula (for stirring ganache and dough)
- Plastic wrap or lid (to cover and chill ganache)
- Whisk (for dry ingredients)
- 3 Tablespoon cookie scoop
- Baking sheet
- Parchment Paper
- Large round cookie cutter (at least 6 inches wide) or wide glass for shaping (optional)
- Cooling rack
Ingredients
For the cookies
- 170 g unsalted butter ¾ cup, softened
- 150 g brown sugar ¾ cup
- 100 g white sugar ½ cup
- 2 teaspoon vanilla extract
- 1 large egg
- 1 large egg yolk
- 100 g sourdough discard ⅓ cup
- 250 g creamy peanut butter 1 cup
- 270 g all-purpose flour 2 ¼ cups
- 1 teaspoon baking soda
- ½ teaspoon fine sea salt
- 67 g sugar ⅓ cup, for rolling the dough balls
- ¼ teaspoon instant espresso powder optional
for the ganache
- 4 oz semi-sweet or bittersweet chocolate chips about ¾ cup
- 80 ml heavy cream ⅓ cup
- 14 g unsalted butter 1 tbsp
Instructions
- Make the ganache: Heat the cream until steaming (do not boil). Pour over the chocolate chips and butter in a heatproof bowl. Let sit for 2–3 minutes, then stir until smooth. Cover and refrigerate for 1–2 hours, or until firm enough to scoop. Scoop into 1-teaspoon portions and keep chilled while you prepare the cookie dough. Preheat the oven to 350°F (175°C).
- Cream the butter & sugars: In a large bowl, beat the butter, brown sugar, and white sugar until light and fluffy (2–3 minutes).
- Add wet ingredients: Mix in the vanilla, egg, and egg yolk until smooth. Stir in the sourdough discard and peanut butter until fully combined.
- Add dry ingredients: In a separate bowl, whisk together the flour, baking soda, and salt. Mix into the wet ingredients just until no streaks of flour remain. No need to chill.
- Assemble the cookies: Scoop 3-tablespoon portions of dough (about 60g each). Flatten slightly, place a chilled (1-teaspoon) ganache scoop in the center, and wrap the dough around to seal. Roll each dough ball in granulated sugar.
- Bake: Arrange cookies on a lined baking sheet and gently press them down with a fork to help them flatten while baking. They don't need to be totally flat, just not round as these don't spread much. Bake for 10–12 minutes, until edges are set but centers still look soft.
- Cool: Scoot the hot cookies around with a large round cookie cutter to make them perfectly round if preferred. Let cookies rest on the tray for 5 minutes, then transfer to a wire rack to cool completely.
Notes
- NOTE: I bake by weight for accuracy. Cup measurements are approximate and may vary depending on how you scoop.
- I use a 3-tablespoon cookie scoop to portion these, which makes 60g balls of cookie dough. You can also use a 2-tablespoon cookie scoop, which makes 40g dough balls, and this would yield around 30-35 cookies.
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