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Chocolate Thumbprint Cookies with Ganache Recipe

If you’re on the hunt for a cookie that’s chocolatey, fudgy, and just plain irresistible, you’re going to adore this Chocolate Thumbprint Cookies with Ganache Recipe. I absolutely love how these cookies come out with that soft, rich chocolate base and a silky ganache center that oozes decadence in every bite. When I first tried this recipe, I was hooked instantly — and I can’t wait to share all my tips with you so you nail it just as perfectly in your kitchen.

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Why You’ll Love This Recipe

  • Perfect Chocolate Flavor: The Dutch-process cocoa powder delivers a deep, rich chocolate taste that isn’t too bitter or sweet.
  • Simple Yet Elegant: With just a few pantry staples and an easy ganache, these cookies look like they belong at a fancy bakery.
  • Customizable Ganache Center: You can switch up the chocolate type or add sprinkles for fun textures and flair.
  • Great Make-Ahead Option: The dough chills well, and the finished cookies keep beautifully for gifting or snacking later.

Ingredients You’ll Need

This recipe pairs classic baking ingredients with the star of the show: chocolate in two glorious forms. Using brown sugar adds that hint of molasses which compliments the cocoa perfectly, while the egg yolks help keep the texture tender but structured. The ganache is ridiculously simple but so luxurious.

Flat lay of a small mound of all-purpose flour, a small white ceramic bowl filled with dark Dutch process cocoa powder, a small white ceramic bowl containing white baking powder sprinkled lightly, two whole brown eggs with clean shells, a small white ceramic bowl of light brown sugar, a small white ceramic bowl of granulated white sugar, a block of unsalted butter with a smooth surface, a small white ceramic bowl holding semi-sweet chocolate chips, a small white ceramic bowl filled with heavy whipping cream, and a small white ceramic bowl with colorful round nonpareil sprinkles, all arranged symmetrically and balanced on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997 - Chocolate Thumbprint Cookies with Ganache, decadent chocolate cookies, easy chocolate cookie recipe, homemade chocolate thumbprint cookies, rich ganache-filled cookies
  • All-purpose flour: Make sure to spoon and level or better yet, weigh your flour for perfect cookies every time.
  • Dutch-process cocoa powder: This gives a smoother, darker chocolate flavor than natural cocoa.
  • Salt: Just a pinch to enhance all the chocolatey goodness.
  • Baking powder: Helps the cookies stay tender and gives a slight lift.
  • Unsalted butter: Softened but not melted – key for the right dough consistency.
  • Light brown sugar: Packed for moisture and that subtle caramel flavor.
  • Granulated white sugar: For a touch of crispness on the outside.
  • Egg yolks: At room temperature for best mixing and texture.
  • Vanilla bean paste or extract: Enhances the chocolate with warm, aromatic notes.
  • Semi-sweet chocolate chips: For melting into the ganache center.
  • Heavy whipping cream: Heated just right to create a smooth, luscious ganache.
  • Nonpareils (optional): Adds a fun pop of color and a tiny crunch as a garnish.
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Note: You’ll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Variations

One of the joys of this Chocolate Thumbprint Cookies with Ganache Recipe is how easy it is to make your own by switching up the ganache or adding mix-ins. I love encouraging you to make this your own—you’ll find that little changes can make it fresh and exciting every time.

  • Raspberry Jam Ganache: I once swapped half the chocolate ganache for a berry jam and my family went crazy for the tart contrast.
  • White Chocolate Ganache: For a sweeter, creamier variation—just use white chocolate chips instead of semi-sweet.
  • Nutty Twist: Sprinkle finely chopped toasted nuts on top of the ganache for extra texture and flavor.
  • Vegan Option: You can try coconut cream instead of heavy cream and vegan chocolate chips to make these dairy-free.

How to Make Chocolate Thumbprint Cookies with Ganache Recipe

Step 1: Prepare and Mix Your Dry Ingredients

Start by lining two baking sheets with parchment paper so you’re ready for the dough balls. In a medium bowl, whisk together your flour, cocoa powder, salt, and baking powder. This step makes sure every cookie has an even chocolate punch and that the leavening is dispersed perfectly. Set this bowl aside while you cream the butter and sugars.

Step 2: Cream Butter and Sugars to Fluffy Perfection

Using an electric mixer, beat the softened butter with brown sugar and granulated sugar for about two minutes. You want the mixture light and fluffy—this is my favorite part because you can immediately see the texture transform, and the smell is just heavenly. Then add the egg yolks and vanilla paste, beating until pale and smooth, about 1-2 minutes.

Step 3: Combine Dry and Wet Ingredients Gently

Now pour the dry ingredients into the butter mixture. Stir or mix just until combined—don’t overwork the dough or the cookies will become tough. The dough may seem a bit sticky but it’s perfect! I find that if it’s too loose, chilling helps a lot.

Step 4: Shape, Indent, and Chill the Cookies

Scoop about one tablespoon of dough per cookie—this recipe makes 34, so get your cookie scooper ready! Roll the dough into balls and place on the prepared sheets. Using a 1/4 teaspoon, press gently into each dough ball to create a thumbprint indent. Here’s what I learned: chilling the dough with these indents for at least an hour is key to making sure they hold their shape during baking and don’t spread too much.

Step 5: Bake and Perfect the Centre Indentation

Preheat your oven to 350°F (175°C). Space your dough balls about 1½ inches apart on the sheet. Bake for 9-11 minutes (10 minutes works beautifully for me). While they’re still hot, press the centers again to deepen the indent with your measuring spoon or a small cookie cutter. This step ensures that your ganache filling sits perfectly in place. Let them cool 5 minutes on the sheet, then transfer to a wire rack to cool completely.

Step 6: Make and Add the Decadent Ganache

Put your chocolate chips in a small bowl. Gently heat your heavy cream until just about boiling—either in the microwave or on the stove. Pour the cream over the chocolate and let it sit for a minute. Then stir until silky smooth, that glossy magic you’re after. Spoon about one teaspoon of ganache into each cookie’s thumbprint well, and sprinkle with nonpareils if you want to add a festive touch. Chill in the fridge for 10-15 minutes to set.

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Pro Tips for Making Chocolate Thumbprint Cookies with Ganache Recipe

  • Proper Flour Measurement: Spoon and level flour or weigh it – this prevents dense or dry cookies. It was a game changer for me!
  • Chill Those Dough Balls: Chilling helps keep the cookies thick and prevents the indent from disappearing during baking.
  • Perfect Your Indent Post-Bake: Press the centers gently again while warm for a neat, defined thumbprint.
  • Use Quality Chocolate: The ganache shines brightest when you use good-quality chocolate chips for that smooth, shiny finish.

How to Serve Chocolate Thumbprint Cookies with Ganache Recipe

Chocolate Thumbprint Cookies with Ganache Recipe - Serving

Garnishes

I usually stick with classic nonpareils because they add a cute, festive look and a slight crunch that’s fun to bite into. But fresh mint leaves or a tiny dusting of cocoa powder also work beautifully if you’re going for a more sophisticated presentation.

Side Dishes

These cookies pair so well with a big mug of coffee or a creamy hot chocolate. I also love them alongside fresh berries or even a scoop of vanilla ice cream for an extra indulgent treat.

Creative Ways to Present

For parties, I like to arrange the cookies on a tiered dessert tray and drizzle some extra melted chocolate across the top. Wrapping a stack in parchment with a ribbon makes for an adorable edible gift that everyone asks about!

Make Ahead and Storage

Storing Leftovers

I keep leftover cookies in an airtight container in the fridge for up to three days. They stay moist and the ganache remains perfectly firm but creamy. Just make sure they’re fully cooled before storing to avoid any sogginess.

Freezing

I have frozen the baked cookies without ganache before—just freeze them in a single layer on a tray, then transfer to a freezer-safe bag. When ready, thaw completely before adding the ganache. This way, you can prep in advance but keep that fresh ganache shine.

Reheating

If you want to warm them a bit, a few seconds in the microwave does the trick, but be careful not to melt the ganache too much. I usually prefer to eat them cool or at room temperature so the ganache stays perfectly silky.

FAQs

  1. Can I use natural cocoa powder instead of Dutch-process in the Chocolate Thumbprint Cookies with Ganache Recipe?

    You can substitute natural cocoa powder, but know that the flavor will be slightly more acidic and the color lighter. Dutch-process is preferred here for its smooth, mellow taste and rich color, but natural cocoa will still work in a pinch.

  2. Why do the thumbprints lose their indent during baking and how do I prevent it?

    This happens because the dough spreads when warm. To prevent this, chill the dough balls with the indents for at least an hour before baking. Also, press the indent again gently while the cookies are still warm for perfect wells.

  3. Can I make the ganache ahead of time?

    Yes! Ganache can be made a day in advance and stored in the fridge. Before spreading in the cookies, gently warm it up until scoopable and stir well to regain that smooth texture.

  4. How do I make this recipe vegan?

    Swap the butter for vegan butter and use flax egg or other egg replacers instead of egg yolks. For the ganache, use coconut cream and dairy-free chocolate chips. Texture will be slightly different but still delightful.

Final Thoughts

I have to say, this Chocolate Thumbprint Cookies with Ganache Recipe has become one of my go-to treats whenever I want something special but not too complicated. It’s got the richness of a fudgy chocolate cookie with that luscious, creamy ganache center that makes every bite feel like a little celebration. I encourage you to try this one out, whether for a weekend baking session or to impress at your next gathering—trust me, you’ll love the smiles it brings around your kitchen table!

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Chocolate Thumbprint Cookies with Ganache Recipe

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.5 from 119 reviews
  • Author: Villerius
  • Prep Time: 15 minutes
  • Cook Time: 10 minutes
  • Total Time: 1 hour 25 minutes
  • Yield: 34 cookies
  • Category: Dessert
  • Method: Baking
  • Cuisine: American

Description

These Chocolate Thumbprint Cookies are rich, fudgy, and coated with a smooth chocolate ganache center. Perfectly soft with a slight crisp edge, these cookies combine a cocoa-infused cookie base with a luscious chocolate ganache filling for an irresistible treat that’s simple enough for any baker to make.


Ingredients

For the Chocolate Thumbprint Cookies

  • 1 1/2 cups (188 g) all-purpose flour, spooned and leveled
  • 1/2 cup (40 g) cocoa powder, Dutch process
  • 1/2 tsp salt
  • 1/2 tsp baking powder
  • 3/4 cup (168 g) unsalted butter, softened
  • 3/4 cup (165 g) light brown sugar, packed
  • 1/4 cup (50 g) granulated white sugar
  • 2 egg yolks, at room temperature
  • 1 1/2 tsp vanilla bean paste or extract

For the Chocolate Ganache

  • 1 cup (200 g) semi-sweet chocolate chips
  • 1/2 cup (120 ml) heavy whipping cream
  • nonpareils for sprinkling on top, optional


Instructions

  1. Prepare the dough: Line two baking sheets with parchment paper and set aside. In a medium bowl, whisk together the flour, cocoa powder, salt, and baking powder until combined.
  2. Cream the butter and sugars: In a large bowl, use an electric mixer to cream the softened butter with the brown sugar and white sugar for about two minutes until light and fluffy.
  3. Add egg yolks and vanilla: Mix in the egg yolks and vanilla bean paste or extract until the mixture is pale in color and fluffy, about 1-2 minutes.
  4. Combine wet and dry ingredients: Gradually add the dry ingredients to the butter mixture and mix just until combined. Avoid overmixing to keep the dough tender.
  5. Form dough balls and indent: Scoop approximately 1 tablespoon portions of dough (about 34 in total), roll them into balls, and place on the prepared baking sheets. Using a 1/4 tsp, gently press down on each dough ball to create an indent for the ganache filling.
  6. Chill the dough: Refrigerate the indented dough balls on a baking sheet for at least one hour to firm up and prevent spreading during baking.
  7. Bake the cookies: Preheat the oven to 350°F (175°C). Arrange chilled dough balls about 1 1/2 inches apart on baking sheets. Bake for 9-11 minutes, ideally 10 minutes, until the edges are set but centers remain soft.
  8. Refine the indents and cool: Immediately after baking, press down again on each cookie’s center with a 1/4 tsp to restore the indent shape, using a circular cookie cutter if desired. Let cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.
  9. Make the ganache: Place chocolate chips in a small bowl. Heat the heavy cream until just about boiling, then pour over the chocolate chips. Let sit for 1 minute, then stir until smooth and glossy.
  10. Assemble the cookies: Spoon about 1 tsp of ganache into each cookie indent, adding more if needed. Optionally, sprinkle with nonpareils on top for decoration. Chill the completed cookies in the fridge for 10-15 minutes to set the ganache.
  11. Store properly: Keep leftovers in an airtight container in the refrigerator for up to three days to maintain freshness and ganache firmness.

Notes

  • Measure flour properly by spooning it into your cup and leveling it off or by weighing to avoid too dense cookies.
  • Chilling the dough for at least an hour is important to maintain cookie shape and prevent spreading during baking.
  • The ganache can be made ahead and stored in the fridge; rewarm gently before filling cookies if needed.
  • For a decorative touch, use colored nonpareils or sprinkle coarse sea salt on the ganache before chilling.

Nutrition

  • Serving Size: 1 cookie
  • Calories: 120
  • Sugar: 10 g
  • Sodium: 70 mg
  • Fat: 7 g
  • Saturated Fat: 4 g
  • Unsaturated Fat: 2.5 g
  • Trans Fat: 0 g
  • Carbohydrates: 14 g
  • Fiber: 1.5 g
  • Protein: 2 g
  • Cholesterol: 35 mg

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