Name: Chocolate Thumbprint Cookies with Ganache Recipe
Prep time: 15 min
Cook time: 11 min
Total time: 1 h 26 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 comforting about biting into rich, buttery cookies filled with silky chocolate— and that’s exactly why I’m excited to share my Chocolate Thumbprint Cookies with Ganache Recipe with you. These treats bring the perfect balance of soft cocoa cookie dough and luscious ganache that melts in your mouth.

The image shows round, dark brown chocolate cookies with a shiny, smooth chocolate center in each one, decorated with small red, green, and white round sprinkles. The cookies are placed closely on a white wooden board with a few visible wood grain textures. To the side, there is a part of a white plate holding more of the same cookies. The background is a white marbled texture with a red ribbon partially visible on the left side. 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 honestly can’t get enough of these cookies. When I first made this Chocolate Thumbprint Cookies with Ganache Recipe, I was amazed by how easy it was to get professional-level results right in my kitchen. Plus, they’re a total crowd-pleaser — whether for a cozy night in or gifting during the holidays.

Perfect texture combination: The crumbly, chocolatey cookie paired with smooth, rich ganache is simply irresistible.
Simple ingredients: You likely have everything at home already, making it easy to whip up whenever you want.
Customizable flavors: You can tweak the intensity of cocoa or add decorative touches to match any occasion.
Make ahead friendly: The dough and ganache freeze beautifully so you can prep ahead of time.

The image shows many round dark chocolate cookies arranged closely on a white marbled surface. Each cookie has one thick layer of shiny dark chocolate filling in the center, topped with small round sprinkles in red, white, and green colors. At the top of the image, there is a white bowl filled with the same colorful sprinkles. The cookies have a smooth but slightly textured edge, and the chocolate center looks glossy and smooth, reflecting light. The sprinkles scattered on the filling add a festive touch, with red, green, and white dots spread evenly. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

This recipe uses ingredients that come together beautifully, balancing flavor and texture perfectly. I always tell friends that paying attention to things like cocoa powder quality and butter temperature really makes a difference.

Flat lay of a small mound of all-purpose flour on a simple white ceramic plate, a small white ceramic bowl filled with rich Dutch process cocoa powder, a small white ceramic bowl of fine white granulated sugar, a small white ceramic bowl containing packed light brown sugar, two whole brown eggs with smooth clean shells, a chunk of softened unsalted butter on a white ceramic dish, a small white ceramic bowl holding glossy semi-sweet chocolate chips, a small white ceramic bowl filled with thick heavy whipping cream, and a vanilla bean pod placed neatly beside the bowl of eggs, arranged in perfect symmetry 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 but is light enough to keep cookies tender.
Dutch-process cocoa powder: Rich in flavor and less acidic, it gives a deep chocolate taste without bitterness.
Salt: Enhances all the chocolate and sweetness, balancing flavors.
Baking powder: Helps the cookies rise just enough for a delicate crumb.
Unsalted butter: Adds creaminess and controls salt level so you can season exactly right.
Light brown sugar: Brings moisture and subtle caramel notes to the dough.
Granulated sugar: Adds crispness and sweetness for balance.
Egg yolks: Keep the cookies tender and rich – don’t replace with whole eggs, or you’ll lose that soft texture.
Vanilla bean paste or extract: Amplifies all the other flavors with a warm, aromatic hint.
Semi-sweet chocolate chips: For luscious ganache filling; their melting quality makes a smooth finish.
Heavy whipping cream: Combines with chocolate to make that silky ganache with just the right richness.
Nonpareils (optional): A fun decorative touch that gives a little crunch and playful color.

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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.

Make It Your Way

One of my favorite parts about this Chocolate Thumbprint Cookies with Ganache Recipe is how customizable it is. I sometimes swap the semi-sweet chips for dark chocolate or add a pinch of espresso powder to intensify the chocolate flavor.

Variation: I once made these with crushed peppermint in the ganache for a festive twist, and they were a hit at Christmas parties.

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

Step 1: Whisk Dry Ingredients Together

I always start by gently whisking the flour, Dutch-process cocoa powder, salt, and baking powder in a medium bowl. This helps the leavening distribute evenly and prevents clumps of cocoa, ensuring a uniform chocolate color and flavor throughout your cookies.

Step 2: Cream Butter and Sugars

Next, I use my electric mixer to cream the softened butter with brown and white sugars for a couple minutes until fluffy and pale. This step is key for light, tender cookies because it creates tiny air pockets in the dough.

Step 3: Add Yolks and Vanilla

I beat in the egg yolks and vanilla until the mixture looks silky and lighter in color. This richness makes the cookies melt in your mouth, plus the vanilla deepens the chocolate flavor.

Step 4: Combine Wet and Dry

Then, I slowly add the dry ingredients just until combined—overmixing chops the delicate texture. The dough will feel soft but easily holds its shape once scooped.

Step 5: Shape and Indent the Cookies

Using a small cookie scoop or tablespoon, I portion the dough into about 34 balls. Here’s a tip: use the back of a measuring spoon (I find ¼ teaspoon perfect) to gently press a shallow well in each ball — this is where that luscious ganache will go later!

Step 6: Chill the Dough

This chilling step is crucial. I refrigerate the cookie dough balls for at least one hour before baking. It helps prevent spreading and keeps those thumbprints defined so the ganache sits perfectly.

Step 7: Bake and Shape Again

After preheating the oven to 350°F (175°C), I space the cookies about 1 ½ inches apart on parchment-lined sheets and bake them for about 10 minutes. Once out of the oven, I softly press the centers again with my measuring spoon to ensure the indent doesn’t disappear during cooling. A circular cookie cutter is great to gently round any irregular edges while they’re still warm.

Step 8: Make the Ganache

While cookies cool, I melt semi-sweet chocolate chips with warm heavy cream. Pouring the hot cream over chocolate and letting it rest before stirring helps the ganache come out silky smooth every time.

Step 9: Fill and Chill Cookies

I dollop about 1 teaspoon of ganache into each cookie's well, topping with nonpareils for a festive crunch if I’m feeling playful. Then, a quick chill in the fridge sets them beautifully for about 10-15 minutes.

Top Tip

Over the years, I’ve learned a few little tricks that take this Chocolate Thumbprint Cookies with Ganache Recipe from good to unforgettable, and I want to share those sweet secrets with you!

Proper flour measuring: Spoon your flour into your measuring cup and level it off — no scooping! This prevents dry, crumbly cookies.
Don’t skip chilling: I’ve tried baking without chilling the dough and the cookies spread too much, losing that perfect thumbprint shape.
Press the centers post-bake: Pressing the cookie centers immediately after baking helps them regain the perfect indentation for the ganache.
Use quality chocolate: Investing in good semi-sweet chocolate chips makes your ganache smoother and richer.

How to Serve Chocolate Thumbprint Cookies with Ganache Recipe

Chocolate Thumbprint Cookies - Serving Suggestion

Garnishes

I love to keep it simple with a sprinkle of colorful nonpareils or just a dusting of cocoa powder on top. For special occasions, a light pinch of sea salt on the ganache adds a beautiful flavor contrast that never fails to impress guests.

Side Dishes

These cookies pair wonderfully with a warm cup of coffee or a glass of cold milk. For a party, I sometimes serve them alongside fresh berries or vanilla ice cream to balance the rich chocolate.

Creative Ways to Present

For birthdays or holidays, I arrange the cookies on decorative trays with mint sprigs or edible flowers for a lovely gift presentation. Wrapping them in cellophane bags tied with ribbon always scores bonus points for gifting.

Make Ahead and Storage

Storing Leftovers

I store leftover cookies in an airtight container at room temperature for up to three days. If you notice the ganache softening too much, just pop them in the fridge briefly before serving.

Freezing

The dough freezes perfectly — I shape and indent the balls, then freeze them on a tray before transferring to a freezer bag. You can bake them straight from frozen, just add a couple of minutes to the bake time. Ganache-filled finished cookies freeze well too if stored airtight.

Reheating

If your cookies have chilled in the fridge, I usually warm them for 10-15 seconds in the microwave to soften the ganache before enjoying. Just be careful not to heat too long, or the cookie gets too soft.

Frequently Asked Questions:

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

While you can use regular cocoa powder, Dutch-process cocoa has a smoother, less acidic flavor that really enhances the cookies. If you do swap, expect a slightly different color and taste.

How do I keep the thumbprints from disappearing during baking?

Chilling the dough for at least an hour helps maintain shape, and pressing the centers again right after baking ensures the indent stays perfect for the ganache.

Can I make this recipe dairy-free?

Yes! You can substitute dairy-free butter and use a dairy-free heavy cream alternative for the ganache. The texture may vary slightly, but it’ll still be delicious.

How long does the ganache take to set?

Chilling the ganache-filled cookies in the fridge for about 10-15 minutes is usually enough for the ganache to firm up and hold its shape.

Final Thoughts

This Chocolate Thumbprint Cookies with Ganache Recipe holds a special place in my recipe box — it’s a simple, no-fail way to make any day feel a little more decadent. I love sharing these with friends because they are universally adored and a true labor of love. I hope you enjoy making (and eating) them as much as I do!