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Chocolate Thumbprint Cookies – Soft, Fudgy & Filled With Silky Chocolate

These Chocolate Thumbprint Cookies are a chocolate lover’s dream — soft, fudgy, and beautifully filled with a creamy chocolate ganache center. Inspired by the beloved In Bloom Bakery style, these cookies combine rich cocoa, deep brown sugar sweetness, and a melt-in-your-mouth texture that delivers pure decadence in every bite. The edges bake up tender, the centers stay luxuriously soft, and the smooth ganache filling creates the perfect contrast of texture and flavor. Whether you’re baking for holidays, gifting cookie boxes, or treating yourself to something special, these elegant thumbprints always impress. Their shape makes them ideal for decorating with nonpareils, crushed peppermint, sprinkles, or a simple drizzle of extra chocolate. Let’s dive into the ultimate chocolate-forward cookie experience!
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Prep Time 15 minutes
bake & Cooling + filling time time 32 minutes
Total Time 47 minutes
Servings: 26 cookies
Ingredients Equipment Method Notes
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Ingredients
  

Fresh Products
  • 2 Egg yolks
Dry & Flavoring Ingredients
  • 1 1/2 cups All-purpose flour
  • 1/2 tsp Baking powder
  • 3/4 cup Light brown sugar packed
  • 1/2 cup Dutch-process cocoa powder
  • 1/2 tsp Salt
  • 1/4 cup Granulated sugar for rolling
  • 1 cup Semi-sweet chocolate chips
  • 1 1/2 tsp Vanilla bean paste or extract
Dairy
  • 3/4 cup Unsalted butter softened
  • 1/2 cup Heavy whipping cream
Desserts
  • Nonpareils optional, for decorating
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Equipment

  • Mixing bowls
  • Hand mixer or stand mixer
  • Baking sheet
  • Parchment paper
  • Rubber spatula
  • Measuring cups & spoons
  • Saucepan (for ganache)
  • Small cookie scoop
  • Cooling rack

Method
 

step1:
  1. Preheat your oven to 350°F (175°C). Line your baking sheet with parchment paper and set aside.
step2:
  1. In a medium bowl, whisk together the flour, cocoa powder, baking powder, and salt. This ensures even distribution of the dry ingredients.
step3:
  1. In a large mixing bowl, cream together the unsalted butter and brown sugar for 2–3 minutes, until light and fluffy.
step4:
  1. Add the egg yolks and vanilla bean paste to the butter mixture. Mix until smooth and creamy.
step5:
  1. Gradually add the dry ingredients to the wet ingredients, mixing on low speed until a thick dough forms.
step6:
  1. Scoop dough into 1-tablespoon portions, roll into smooth balls, and then roll each ball lightly in granulated sugar.
step7:
  1. Place on the baking sheet, spaced 2 inches apart. Use your thumb (or the back of a teaspoon) to gently press a well into the center of each cookie.
step8:
  1. Bake for 10–12 minutes, or until the edges are set but the centers remain soft. Immediately reinforce the thumbprint indentation after baking if needed.
step9:
  1. Prepare the ganache: In a saucepan, heat the heavy cream until steaming (not boiling). Pour over the chocolate chips, let sit 1 minute, then stir until smooth and glossy.
step10:
  1. Spoon or pipe the warm ganache into the center of each cookie. Add nonpareils or sprinkles for decoration if desired.
step11:
  1. Cool completely on a wire rack until the ganache sets.

Notes

🧊 Storage & Reheating
Store in an airtight container at room temperature for 5 days.
Refrigerate for up to 1 week.
Freeze (unfilled or filled) for 2 months.
To serve from frozen: thaw at room temperature for 20 minutes.
🥄 Variations
Peppermint Version – Add 1/4 tsp peppermint extract to the cookie dough and sprinkle crushed candy canes on top.
Salted Chocolate – Add flaky salt on the ganache before it sets.
Hazelnut Ganache – Add 2 tbsp hazelnut spread to the melted chocolate.
Mocha Thumbprints – Add 1 tsp espresso powder to the cocoa mixture.
White Chocolate Center – Swap semi-sweet chips for white chocolate.
❓ 10 FAQs
1. Why use egg yolks instead of whole eggs?
They create a richer, fudgier cookie texture.
2. Can I use natural cocoa instead of Dutch-process?
Dutch-process gives a deeper flavor and darker color — but natural cocoa works too.
3. Why did my cookies crack?
Pressing too deeply before baking can cause cracking; press gently.
4. Can I make them without ganache?
Yes — fill with jam, caramel, or peanut butter instead.
5. How do I keep the cookies soft?
Store with a slice of bread or marshmallow; they absorb excess dryness.
6. Can I double the recipe?
Absolutely — these freeze beautifully.
7. Can I color the ganache?
Use white chocolate + gel coloring for vibrant centers.
8. Why reroll in sugar?
It adds sparkle, sweetness, and slight crunch.
9. Should ganache be warm or cooled?
Warm is best — it fills the indent smoothly.
10. Can I freeze the dough?
Yes — freeze scooped balls, then bake straight from frozen (add 2 minutes).
🏁 Conclusion
These Chocolate Thumbprint Cookies are the perfect mix of elegance and indulgence — soft, rich, and filled with silky chocolate ganache. They’re ideal for gifting, holiday trays, or simply spoiling yourself with a gourmet-style cookie made right at home.
Expect compliments… and requests for the recipe!