Name: Chocolate Thumbprint Cookies with Ganache Recipe
Prep time: 15 min
Cook time: 10 min
Total time: 1 h 25 min
Cuisine: American
Ingredients: 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; 1 cup (200 g) semi-sweet chocolate chips; 1/2 cup (120 ml) heavy whipping cream; Nonpareils for sprinkling on top, optional

There’s something so charming about these little bites of heaven—soft, cocoa-rich cookies with a luscious pool of glossy chocolate in the center. This Chocolate Thumbprint Cookies with Ganache Recipe is one of those recipes I find myself coming back to whenever I want to impress with minimal effort but maximum wow.

The image shows several round dark chocolate cookies arranged on a white wooden serving board with a light wood grain. Each cookie has two layers: the base layer is a thick, soft-looking dark brown chocolate cookie with a slightly rough texture around the edges, and the center layer is a glossy dark chocolate ganache filling that is smooth and shiny. On top of the ganache, there are small round sprinkles in red, green, white, and light blue colors scattered evenly. A white plate with more cookies is partly visible on the left, resting on a white marbled surface, and a small bowl filled with the same colored sprinkles sits in the top right corner. A deep red ribbon is faintly visible on the lower left corner. photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Chocolate Thumbprint Cookies with Ganache Recipe
Top Tip
How to Serve Chocolate Thumbprint Cookies with Ganache Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Chocolate Thumbprint Cookies with Ganache Recipe

Why You'll Love This Recipe

I’ve made a lot of chocolate cookies, but these thumbprints are special because they balance rich cocoa flavor and tender crumb with decadent homemade ganache. The combination always feels like a mini celebration, whether it's for the holidays or an everyday treat.

Perfect Balance: The cocoa in the cookie dough adds depth without overpowering the silky ganache center.
Simple Technique: Creating the indents and filling them is straightforward enough for bakers of all skill levels.
Customizable: You can dress them up with sprinkles, sea salt, or even a touch of chili powder for fun twists.
Great for Gifting: These cookies look gorgeous on a platter and hold up well for packaging.

The image shows many dark chocolate cookies arranged closely together on a white marbled surface. Each cookie has a smooth, shiny layer of dark chocolate in the center, which is topped with small round sprinkles in red, white, and green colors. The cookies have a slightly rough texture around the edges and a glossy center that reflects light. Near the top, there is a small white scalloped bowl filled with the same red, white, and green sprinkles, adding a festive touch to the scene. The overall look is rich and inviting with a contrast between the dark cookies and bright sprinkles. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Let’s talk ingredients – each one brings something vital to the table, creating that irresistible texture and flavor combo. I always recommend using quality cocoa and chocolate for the ganache to keep the flavor top-notch.

Flat lay of a small mound of all-purpose flour on a simple white ceramic plate, a small white ceramic bowl filled with dark Dutch process cocoa powder, a few small piles of light brown sugar and granulated white sugar side by side on a white ceramic dish, two whole uncracked brown eggs with clean shells resting on the surface, a small white bowl of unsalted softened butter, another small white ceramic bowl containing glossy semi-sweet chocolate chips, a small white bowl filled with heavy whipping cream, and a few loose nonpareils scattered neatly on the white marble surface, all arranged with perfect symmetry and balanced proportions, placed 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

All-purpose flour: Provides structure so the cookies hold their soft but sturdy form. I always spoon and level to avoid dense cookies.
Dutch-process cocoa powder: This gives a deep, rich chocolate flavor and tenderness to the dough.
Salt: Balances sweetness and enhances the chocolate notes beautifully.
Baking powder: Gives a slight lift ensuring the cookies aren’t too dense.
Unsalted butter: Softened for creaming, it’s the base of richness and tenderness.
Light brown sugar: Adds a subtle molasses flavor and chewiness.
Granulated white sugar: Balances brown sugar and aids in slight crisp edges.
Egg yolks: Richer than whole eggs, they make these cookies tender and flavorful.
Vanilla bean paste or extract: Deepens flavor layers—vanilla always plays so nicely with chocolate.
Semi-sweet chocolate chips (for ganache): Melts beautifully for that smooth, glossy filling.
Heavy whipping cream: Creates the perfect creamy consistency for the ganache.
Nonpareils (optional): Fun little sprinkles to add color and texture on top.

📝

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.

Make It Your Way

While I adore these cookies as-is, I love mixing things up depending on the occasion. You truly can make this Chocolate Thumbprint Cookies with Ganache Recipe your own with a few tweaks and additions.

Variation: Sometimes I swap the semi-sweet chocolate ganache for a salted caramel filling—it adds a dreamy sweet-salty contrast that’s irresistible.
Dietary tweak: For a gluten-free option, I’ve successfully used a 1-to-1 gluten-free baking flour instead of all-purpose flour. Just be cautious with chilling times as the dough texture changes slightly.
Seasonal twist: Adding a pinch of cinnamon or chili powder to the dough gives these cookies a warm kick that’s perfect for winter holidays.

Step-by-Step: How I Make Chocolate Thumbprint Cookies with Ganache Recipe

Step 1: Whisk together dry ingredients

Start by sifting or whisking together the flour, cocoa powder, salt, and baking powder in a medium bowl. Getting the dry stuff fully combined here makes the dough smooth and avoids uneven pockets of cocoa or leavening.

Step 2: Cream butter and sugars

In a large bowl, beat your softened butter with both the brown and granulated sugars until light and fluffy—this usually takes about two minutes with an electric mixer. This step is key for that tender, almost melt-in-your-mouth texture.

Step 3: Add egg yolks and vanilla

Mix in the egg yolks and vanilla paste until the batter looks pale and fluffy—this helps the cookies rise gently and adds richness. Don’t skip making sure your yolks are at room temp; it really helps mixing.

Step 4: Incorporate dry ingredients just until combined

Slowly add the flour mixture to the wet ingredients and stir until just combined. Overmixing here can make the cookies tough, so stop as soon as you don’t see dry streaks.

Step 5: Shape and indent the dough balls

Divide the dough into about 34 equal portions and roll them into balls — roughly a tablespoon each. Place them on parchment-lined baking sheets, spaced comfortably apart. Then use a ¼ teaspoon measure to press a small indent into the center of each ball. This creates your “thumbprint” ready to hold the ganache.

Step 6: Chill the dough

Chill these dough balls with indentations for at least an hour. I find this step helps cookies maintain their shape during baking and lets the flavors develop. You can chill them all on one tray and separate before baking.

Step 7: Bake to perfection

Preheat your oven to 350°F (175°C). Arrange the chilled dough balls about 1 ½ inches apart and bake for 9 to 11 minutes—10 minutes hits the sweet spot for me. Right when they come out, press the centers again to refresh those indents if they’ve puffed up slightly, and run a small circular cutter gently around each to shape them perfectly. Let cool on the sheet for 5 minutes before moving to a wire rack.

Step 8: Make the ganache

Gently heat your heavy cream until just about to boil, then pour it over the chocolate chips in a bowl. Let it sit undisturbed for one minute, then stir until silky smooth. This simple ganache filling is the star of the show.

Step 9: Fill and chill the cookies

Use a teaspoon to fill each thumbprint well with luscious ganache. If you want, sprinkle tiny nonpareils or a pinch of sea salt atop for a little extra flair. Pop the cookies into the fridge for 10-15 minutes so the ganache sets up firm but still creamy.

Top Tip

Through baking this cookie dozens of times, I’ve learned some little tricks that make all the difference for success and flavor every single time.

Accurate Flour Measurement: Don't scoop directly from the bag; spoon flour into your cup or weigh it. Too much flour makes these cookies dry and crumbly.
Room Temperature Yolks: Helps create a smoother dough and better texture—just set your eggs out early or warm cups of water to speed it up.
Indent Deep Enough: Press firmly but gently; too shallow and the ganache may spill over, too deep and you’ll lose cookie shape.
Repress Centers Warm: Right out of the oven, the dough is pliable—reshaping those indents calms any puffiness and keeps presentation neat.

How to Serve Chocolate Thumbprint Cookies with Ganache Recipe

chocolate thumbprint cookies - Serving Suggestion

Garnishes

I’m a sucker for a sprinkle of festive nonpareils or a few flakes of sea salt on top of the ganache—those little finishing touches make the flavor pop and the cookies look extra special.

Side Dishes

I love pairing these cookies with a creamy vanilla ice cream or a bold cup of espresso. If you want to turn them into an after-dinner treat, serve with fresh berries or a drizzle of raspberry coulis.

Creative Ways to Present

For parties, I arrange them on decorative platters with edible flowers or mix with other cookie varieties for a cookie board. Wrapping a stack in parchment tied with twine makes for darling homemade gifts.

Make Ahead and Storage

Storing Leftovers

I store leftover cookies in an airtight container layered with parchment paper at room temperature for up to three days. This keeps the cookies tender and ganache perfectly set without drying out.

Freezing

I’ve had great success freezing unfilled cookie dough balls or fully baked cookies (without ganache). For the filled ones, I freeze them after the ganache sets, wrapped tightly in plastic wrap and stored in a container. Just thaw at room temp before serving.

Reheating

Generally, I don’t recommend reheating these cookies as the ganache can soften too much, but if you want warm chocolate, a quick zap of 10-15 seconds in the microwave works wonders just before serving.

Frequently Asked Questions:

Can I use regular cocoa powder instead of Dutch-process?

Yes, you can use natural cocoa powder if that’s what you have on hand, but be aware it’ll give a brighter, slightly more acidic flavor compared to the smoother, richer taste of Dutch-process. Adjust the baking powder slightly if needed since natural cocoa is more acidic.

How do I prevent the cookies from spreading too much?

Chilling the dough with the indents before baking is key—it firms up the fat in the dough to reduce spreading. Also, make sure your baking sheets are cool and avoid pressing the dough too thin.

Can I use a different type of chocolate for the ganache?

Absolutely! Dark chocolate gives a more intense, bittersweet ganache, while milk chocolate creates a sweeter, creamier center. White chocolate works, too, but be sure to adjust sweetness accordingly.

How long can I store these cookies?

Stored in an airtight container at room temperature, they stay fresh for up to three days. For longer storage, freeze unfilled dough or fully baked, chilled cookies for up to three months.

Final Thoughts

Making these Chocolate Thumbprint Cookies with Ganache Recipe became one of my favorite baking rituals because it’s forgiving, fun, and creates a little moment of pure chocolate bliss. I hope you enjoy making (and eating!) them as much as I do—grab your mixing bowl and dive in, your cookie jar will thank you.