Gluten Free Chocolate Thumbprint Cookies

Chocolate ganache fills the center of these gluten free chocolate thumbprint cookies, which are laced with crunchy turbinado sugar.

chocolate thumbprint cookies on white square plate with blue snowflake napkin

I love a great thumbprint cookie as much as the rest of you might. But I find that when it comes to jam-filled thumbprints, the amount of jam is so minimal it’s just not worth it. That’s why I’d prefer to make my gluten free bow tie cookies because you get jam in every bite!

But in these chocolate thumbprint cookies, the ganache is so rich that the disk in the center of the cookie is exactly the perfect amount of chocolate to not overwhelm the rest of the cookie. The ganache dries to almost a chocolate chip type consistency. Pair that with the crunch obtained from rolling the cookies in turbinado sugar for the ultimate chocolate “kiss” cookie!

The Ingredients in Gluten Free Chocolate Thumbprint Cookies

  • Kim’s gluten free flour blend–a store bought blend, such as Cup4Cup, can be substituted.
  • Butter–if you have no aversions, butter is always better (in my opinion at least).
  • Granulated sugar
  • Brown sugar
  • Egg yolks–add richness and moisture
  • Baking powder–adds a little rise to the cookies
  • Vanilla extract
  • Salt
  • Turbinado sugar–for dredging

Rolling the Cookies

I like to use a small cookie scoop like this one to scoop out just enough dough for consistently sized cookies. Roll them between your palms to smooth them into perfect one-inch balls, and dredge them in turbinado sugar. If you don’t have turbinado, you can also use sanding sugar or just plain ‘ole granulated sugar.

rolling balls of dough in turbinado sugar

Making the Ganache

Melt the chocolate over a double boiler (a simple heat-proof bowl set over a pan of simmering water) along with cream, butter, and corn syrup. Stir until smooth and all the chocolate is completely melted. Allow the ganache to cool before filling the centers of the cookies.

The ganache for these cookies is a little different than a usual ganache. It’s very thick, which is what we want when it dries because it’ll stay put and act almost like a Hershey’s kiss! In fact, you could probably use a Hershey’s kiss instead of making the ganache if you want!!

filling cookies with chocolate ganache

These gluten free chocolate thumbprint cookies are a deviance from the jam-filled ones you’ve know about forever, but they’re filled with chocolate so who wouldn’t love them?

chocolate thumbprint cookies on white square plate with blue snowflake napkin

Gluten Free Chocolate Thumbprint Cookies

Chocolate ganache fills the center of these gluten free chocolate thumbprint cookies, which are laced with crunchy turbinado sugar.
4.50 from 4 votes
Prep Time 20 minutes
Cook Time 12 minutes
Course Dessert
Cuisine American
Servings 40 cookies


  • 2 cups (280 g) Kim's gluten free flour blend (a store bought blend may be substituted)
  • ½ tsp baking powder
  • ¼ tsp salt
  • 1 cup (2 sticks or 226 g) butter, softened
  • ½ cup (100 g) granulated sugar
  • ¼ cup (50 g) brown sugar
  • 2 large egg yolks
  • 1 tsp vanilla extract
  • cup turbinado sugar (sanding sugar or granulated sugar may be substituted)

Chocolate Ganache

  • 6 ounces ( chopped bittersweet or semi-sweet chocolate
  • 2 tbsp heavy whipping cream
  • 1 tbsp corn syrup
  • 1 tbsp butter


  • 1 package (11 oz or 311 g) Hershey's kisses, unwrapped (or enough unwrapped kisses to fill 40-50 cookies)


  • In a large bowl, cream butter and both sugars until fluffy, about 2 minutes. Add egg yolks and vanilla and beat until well combined. Scrape down sides of bowl.
  • In a separate bowl, mix together flour, baking powder, and salt. With the mixer running on low, slowly add flour mixture into butter mixture until well blended. Cover the bowl and refrigerate until the dough is firm, about 30 minutes.
  • Place the turbinado sugar in a small shallow bowl. Shape the dough into 1-inch balls and roll each in the sugar to coat. Place 1 inch apart on a parchment-lined baking sheet. If using homemade ganache, press your thumb in the center of each ball to make a crevice. If using Hershey's kisses, skip this part and leave the dough in balls.
  • Bake cookies in a 325° F oven until lightly browned, about 10-12 minutes. If the indentations have disappeared, make them again while the cookies are still warm. If using Hershey's kisses, press a kiss in the center of each cookie as soon as they come out of the oven.

Make the Chocolate Ganache

  • While the cookies are baking, make the ganache. In a double boiler (a heat-proof bowl set over a pan of simmering water), melt chocolate with heavy cream, corn syrup, and butter, stirring gently until all the chocolate is melted and the mixture is smooth. Allow the ganache to cool for 10-15 minutes.

Filling the Cookies

  • Fill each cookie with about a teaspoon of chocolate ganache. It will harden like a chocolate chip (or Hershey's kiss) when it cools.


Cookies freeze very well for up to 2 months.  Wrap well before freezing, and leave wrapped when thawing.    
Keyword chocolate, Gluten Free, thumbprint cookies
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