Double Chocolate Thumbprint Cookies

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Double Chocolate Thumbprint Cookies feature the silkiest ganache center you could ever dream of! Nestled right into a soft, chewy cookie, each bite practically melts in your mouth. Have the recipe handy, because everyone will love these thumbprint cookies with a chocolate center!

Titled Image: Chocolate Thumbprint Cookies


Chocolate Thumbprint Cookies

Instead of a more traditional thumbprint cookie with jam or fruit filling, we’re doubling down on sweet cocoa flavor for a chocolate lovers’ dream!

Find it in both the dough and the ganache center for the ultimate chocolate thumbprint cookies recipe.

If you’re looking for a different spin on this classic, check out my Chocolate Cherry Thumbprint Cookies!

Double is always better in my opinion, which is why you’ll find double the chocolate in my pecan brownies, chocolaty buckeye brownie cookies, and Caramel Turtle Trifle.

And if double just isn’t enough for you, try my triple chocolate cookies with both baking chips and chunks!

ingredients for chocolate thumbprint cookies

Ingredient Notes and Substitutions

  • All-Purpose Flour – With so few ingredients, it’s important to be precise!

    Measure your flour with the spoon and level method to ensure the dough is the perfect consistency.
  • Cocoa Powder – I prefer Hershey’s Dark for this double chocolate cookies recipe as the flavor is much deeper.
  • Unsalted Butter – Since every brand of butter contains a different amount of salt, it’s better to use unsalted so there are no texture or flavor surprises.

    If salted butter is all you have on hand, reduce the amount of kosher salt in the dough to ½ teaspoon.
  • Egg – Your dough will mix together much smoother if this and the butter are room temperature before you begin.
  • Instant Coffee Granules – The secret to baking with chocolate! These enhance the rich flavor but won’t make your treats taste like coffee, I promise.
  • Ganache – A simple mixture of melted semisweet chocolate chips and heavy cream. Make it in the microwave!
chocolate thumbprint cookie dough in mixing bowl

Double Chocolate Cookies Recipe Tips and Tricks

  • Mix the dough just until combined.

Don’t think a higher speed on your mixer will get the job done faster! Mix in those dry ingredients on low so you can monitor the progress.

As soon as there are no more streaks of flour, it’s ready to scoop. Mixing longer will only result in dense, dry thumbprint cookies with chocolate.

  • Make perfect wells for the ganache filling.

The best way to make thumbprint indentations in your cookies isn’t actually with your thumb!

Since everyone’s digits are different sizes and shapes, stick with a kitchen tool instead.

A ¼ teaspoon measuring spoon is often the best size — rounded or flat-bottomed spoons (instead of elongated) are even better.

Be sure to indent as soon as the dough is rolled, or you’ll risk the edges cracking.

  • Achieve picture-perfect round cookies. 

Once they’re out of the oven, use a round cookie or biscuit cutter to shape your chocolate thumbprint cookies.

Simply swirl the cutter around each cookie to form a perfect circle.

Move quickly — the edges are much easier to shape while the dough is quite hot!

making a thumbprint in chocolate cookie dough

Storing and Freezing Thumbprint Cookies with Chocolate

Once you’ve added the ganache, these treats can be stored in an airtight container in the refrigerator for 3 to 4 days. 

You can also double this chocolate thumbprint cookies recipe and freeze half of the dough for later!

Wrap tightly in several layers of plastic wrap, then thaw in the refrigerator before baking.

Baked thumbprint cookies can be frozen for up to 3 months, but wait to add the ganache until the day you plan to serve them.

Kitchen Tools You Will Need

  • Baking Sheets lined with parchment paper
  • Mixing Bowls – You’ll need a variety of sizes to make the dough, roll it in sugar, and melt the chocolate for ganache.
  • Stand mixer or large mixing bowl with hand mixer for the dough — don’t try to mix it by hand!
  • A Piping Bag gives you more control over the chocolate and is less messy.

    You can also make your own by filling a plastic storage bag and snipping off the corner opposite from the zippered top.
filling baked chocolate cookies with chocolate ganache

Chocolate Thumbprint Cookies Recipe FAQ

How do I prevent chocolate thumbprint cookies from spreading too much when baking?

First, be sure you followed this double chocolate cookies recipe exactly as written. If the dough is too wet or soft, it’s sure to spread.

It can also help to chill the dough before it goes in the oven. Even better, scoop out the rounds before popping them in the fridge for 20-30 minutes. Then, all you have to do is indent your cookies!

Finally, line your baking sheets with parchment paper or a silpat mat. These prevent baked goods from sticking while also giving the dough something to grip — slowing spread and helping them keep their shape.

Can I customize the fillings for the thumbprint indentations?

You bet! Flavor your ganache with extract — vanilla or peppermint would be tasty — or try a different filling altogether.

Try dark or white chocolate chips instead of semi-sweet, or use vanilla-flavored melted chocolate instead. You can mix in some gel food coloring or buy candy melts in a variety of colors that are ready to use.

And if you prefer a more classic take, cherry pie filling is an excellent pairing for chocolate thumbprint cookies.

chocolate thumbprint cookies on a tray

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closeup of chocolate thumbprint cookie

closeup of chocolate thumbprint cookies

Double Chocolate Thumbprint Cookies

Donna Elick
These Chocolate Thumbprint Cookies are loaded with double the chocolate flavor! Perfect for cookie swaps, holiday gifts, and dessert tables.
5 stars from 2 reviews
Tried this recipe?Please comment and review!
Prep Time 20 minutes
Cook Time 8 minutes
Total Time 28 minutes
Course Dessert
Cuisine American
Method Oven
Servings 24 cookies


  • 2 cups granulated sugar, divided
  • 1 cup unsalted butter, softened
  • 1 large egg
  • 2 teaspoons pure vanilla extract
  • 1 tablespoon instant coffee granules
  • 2 cups all-purpose flour
  • 1/2 cup dark chocolate Hershey’s cocoa powder
  • 1 teaspoon kosher salt
  • 1/2 teaspoon baking soda

Chocolate Filling:

  • 1 cup semi-sweet chocolate chips
  • 1/2 cup heavy whipping cream


  • Preheat the oven to 350°F (175°C) and line 2 cookie sheets with parchment paper or silpat mats.
  • Prepare the Cookie Dough: In a large bowl, cream together 1 cup of sugar and softened butter until light and fluffy (about 3 minutes). Add the egg, vanilla, and coffee granules. Beat until well combined. Add flour, cocoa powder, salt, and baking soda. Mix on low until just combined. Using a small ice cream scoop, form dough balls and roll them in the remaining 1 cup of sugar. Place them on the prepared cookie sheets, a few inches apart. Make an indentation in the center of each cookie using your thumb.
  • Bake the Cookies: Bake in the preheated oven for 8 minutes or until the edges are set. Allow the cookies to cool on the sheets for 3-5 minutes before transferring them to a cooling rack.
  • Prepare the Chocolate Ganache: In a microwave-safe bowl, heat the cream until hot but not boiling (about 1 minute). Pour the hot cream over the chocolate chips. Cover and let it sit for 3 minutes. Remove the cover and whisk until smooth. Let the ganache cool slightly, then spoon it into a piping bag (or a zip-top bag with the corner snipped off).
  • Fill the Cookies: Pipe dollops of ganache into the indentations of the cooled cookies.
  • Allow the Ganache to Set: Let the cookies sit at room temperature for about 1 hour or chill in the refrigerator for 30 minutes to allow the ganache to harden completely.

Donna’s Notes

Store the cookies in an airtight container at room temperature for up to 3 days, or refrigerate for longer freshness.
Get creative with the filling by using different flavored chocolates or adding a sprinkle of sea salt on top of the ganache.


Serving: 1 | Calories: 239cal | Carbohydrates: 30g | Protein: 2g | Fat: 13g | Saturated Fat: 8g | Cholesterol: 34mg | Sodium: 127mg | Sugar: 20g | Fiber: 2g | Calcium: 16mg | Iron: 1mg

All nutritional information is based on third party calculations and is only an estimate. Each recipe’s nutritional value will vary depending on the ingredients used, measuring methods, and portion sizes.

Tried this recipe?Let us know how it was!
Chocolate Thumbprint Cookies - PIN

Originally published December 2023

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  1. 5 stars
    Just pulled these thumbprint cookies out of the oven and oh my goodness they smell amazing!! The recipe was super simple to follow and I am no bake LOL The cookies are delicious!

  2. 5 stars
    These cookies are simply divine! The chocolatey goodness is out of this world. A definite must-try recipe!

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