This easy recipe for Gluten Free Chocolate Thumbprint Cookies is a fabulous base recipe to have on hand. Thumbprint cookies are typical Holiday Cookies filled with jam. But who says you can’t enjoy them year-round? I jazzed them up with toasted marshmallow frosting and garnished them with tiny marshmallows and chocolate sprinkles.
They are a “Must Make” during the Holiday Season but who says they can’t be enjoyed year round. Just like my Gluten Free Hot Cocoa Cookies. The recipe for the Toasted Marshmallow Filling was originally shared with my recipe for my Gluten Free Hot Cocoa Snack Cake and I used this recipe for Gluten Free Thumbprints to use up the leftover frosting.
Recipe Ingredient Notes
Gluten Free Flour: I tested this recipe for Gluten Free Chocolate Thumbprint Cookies with King Arthur Measure for Measure, Bob’s Red Mill 1-to-1 as well as Cup4Cup. While all three gluten free flour blends worked great in this recipe, the dough made with Cup4Cup baked of the smoothest (on the outside). When it comes to shelf life, the cookies made with King Arthur Measure for Measure stayed soft the longest. All those blends do contain xanthan gum.
Cocoa Powder: I use dutch processed cocoa powder in my baking such as Valrhona Cocoa Powder. The dutch-process cocoa powder creates what some people consider a richer, fudgier flavor in baked goods.
Butter: I only use unsalted butter in my recipes. The key is to make sure it is at room temperature before using. The ideal temperature for butter is actually 65F which is a lot colder than many of us consider room temperature. To test if your butter is at room temperature nudge it with your finger. You should see an indent but the butter should not feel like you can poke right through it.
Marshmallow Creme/Fluff: Yes, we are using store-bought Marshmallow Crème/Fluff in this recipe. You will need 7oz of Marshmallow Creme which is roughly a 16oz bag of marshmallows. IF you use Marshmallows instead of the creme, lay them out in an even layer on a foil-lined baking sheet and broil until toasted. Try to stir them together and toast more. Believe me, this will be easier with Marshmallow Creme/Fluff.
What are Thumbprint Cookies?
Thumbprint cookies look very similar to tiny tarts which can be filled with a variety of fillings. Some of them are added before baking while others are added after the cookie has completely cooled.
Thumbprints are original from Sweden, where they are called Hallongrotta. They are made with a simple sugar cookie dough and filled with raspberry jam.
These days fillings vary from caramel sauce, dulce de leche, chocolate ganache to frostings.
How to prevent Thumbprint Cookies from cracking
Thumbprint cookies have the tendency to crack around the corners. To avoid this I recommend shaping them as soon as the dough has been made.
With a medium-sized cookie scoop, portion out a cookie and roll it into a smooth ball. Immediately roll it in granulated sugar and make the imprint about ½ inch deep with the end of a wooden or your thumb. This way the dough will not stiffen up and form a crust that causes the cracks.
Place the indented balls on a parchment-lined baking sheet and once all the dough has been portioned and shaped, place it into the fridge for at least 2hrs to rest (or 1hr in the freezer)
How to bake Gluten Free Chocolate Thumbprint Cookies
When ready to bake, arrange 8-10 gluten free chocolate thumbprint cookies on a sheet tray and bake in your preheated oven for 11-13 minutes or until the edges have been set. The indents will have lost some shape or have puffed up, so use the end of a wooden spoon or spatula to make an indent again into the warm cookies. Allow the cookies to cool completely before filling.
How to make Toasted Marshmallow Frosting
The Toasted Marshmallow Frosting starts with toasting the marshmallow creme/fluff. You can toast it with a kitchen torch or under your broiler. Regardless of which method you choose, make sure to allow for it to cool down before adding to the filling.
- Line a sheet tray with foil and lightly spray with nonstick pan spray. The non stick spray helps to remove the toasted marshmallow creme easily from the tray.
- Remove the Marshmallow Creme from the jar and spread it evenly on your foil-lined sheet tray.
- With a kitchen torch (or your broiler) toast the marshmallow creme to your liking. Make sure to stir the marshmallow a few times.
- Allow for it to cool (especially if you put it under the broiler) before adding it to the rest of the filling.
- In the bowl of your stand mixer fitted with the paddle attachment, combine the butter and the shortening and beat until light and fluffy. Make sure to scrape down the sides and the paddle.
- With the mixer on LOW gradually add in the powdered sugar and continue to mix until all the sugar is incorporated. Add in vanilla extract and milk and mix for one minute.
- Add your toasted Marshmallow Fluff/Creme and mix at medium-high speed for 3 minutes. Your frosting should look similar to cream cheese frosting or a Vanilla American style buttercream.
- Keep the toasted marshmallow filling at room temperature until ready to fill your Chocolate Thumbprint Cookies.
The recipe for Toasted Marshmallow Cream Filling gives you a generous amount to work with. Any leftovers you may have can be stored in the refrigerator for up to 7 days or frozen for up to 2 months. This filling works fabulously for oatmeal cream pies or sandwiched between my Gluten Free Peanut Butter Cookies.
Filling Ideas for Gluten Free Chocolate Thumbprint Cookies
Dark Chocolate Thumbprints: Place 120 grams of dark chocolate chips in a heat-proof bowl. Heat 120ml Heavy Cream over medium heat until it starts to simmer. Pour the cream over chocolate. Let stand for 5 minutes. Stir until smooth. Let stand until mixture is spoonable, about 15 minutes. Once your ganache and your cookies are cooled, use a small spoon to fill the cavities of your thumbprint cookies. Sprinkle with flaky sea salt.
Peppermint Dark Chocolate Thumbprints: Add ⅛th teaspoon of peppermint extract to dark chocolate ganache. A little goes a long way.
Caramelized White Chocolate Thumbprints: Place 100 grams of Valrhona Dulcey into a heat-proof bowl. Heat 50 ml Heavy Cream over medium heat until it starts to simmer. Pour the cream over chocolate. Let stand for 5 minutes. Stir until smooth. Let stand until mixture is spoonable, about 15 minutes. Allow cooling for at least 10 minutes. Your ganache will have a creamy consistency – not runny! Once your ganache and your cookies are cooled, use a small spoon to fill the cavities of your thumbprint cookies. Sprinkle with flaky sea salt to finish.
Classic Chocolate Jam Thumbprints: Fill with your favorite jam such as raspberry jam or strawberry jam.
Caramel Filled Thumbprint Cookies: Use the caramel recipe found here and fill the baked and cooled cookies with it. You can even combine caramel and chocolate ganache.
Frequently asked questions
Can you freeze chocolate thumbprint cookies?
Yes! The unbaked dough freezes beautifully and so do the baked, unfilled cookies. Freeze them in a single layer on a sheet tray before transferring them to an airtight container. Freeze up to 3 months.
Can I make this recipe ahead of time?
To make those cookies ahead of time, I recommend making and shaping the dough and freezing the unbaked cookies until you are ready for them. Baked and filled cookies will be good for up to 5 days when stored at room temperature.
How do I make those chocolate thumbprint cookies with chocolate kisses?
Instead of using a filling, gently press a chocolate kiss in the indent after the cookies have been baked and cooled for 5 minutes. You don’t want to top them with chocolate kisses when they are still very hot or the kisses will melt.
Can I make the recipe for Gluten Free Thumbprint Cookies dairy free?
Yes! Please substitute the butter with your favorite nondairy version.
I don’t have celiac disease, can I make this recipe with “regular” flour?
Yes. Please substitute the gluten free flour with 205 grams of All Purpose Flour.
Baking in grams
I share my recipes in grams and by weight since baking by weight is the most accurate way to bake. Digital Scales are very affordable and very affordable. You can purchase them on Amazon for less than a set of measuring cups. Measuring cups are very inaccurate and can cause significant errors when it comes to baking. Especially since I bake with gluten-free flours which weigh differently than “regular” flours. I do provide some ingredients like spices and leavening agents in measuring spoons.
Note about Ovens and Oven Temperatures
All my recipes are tested and developed with a conventional oven. I always bake my baked goods on the rack placed in the MIDDLE of my oven. This way the heat coming from the bottom will not burn my baked goods.
If you are baking with convection (fan-forced), please adjust the recipes accordingly. Be also prepared that the convection oven can cause your baked goods to dry out quickly and still be raw inside. Be aware that it takes at least 15-20 minutes for a standard American Oven to be fully preheated. I highly recommend investing in an Oven Thermometer.
Substitutions and Modifications
Any dietary or ingredient modifications/substitutions to this recipe may alter the end result in appearance and taste. I test my recipes several times as published in this post and The Gluten Free Austrian Blog is not responsible for the outcome of any recipe you find on our website.
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For Gluten Free Chocolate Thumbprint Cookies
- 230 grams Gluten Free Multipurpose Flour
- 60 grams unsweetened cocoa powder
- ½ teaspoon baking soda
- ½ teaspoon kosher salt
- 1 teaspoon espresso powder
- 113 grams unsalted butter, at room temperature
- 115 grams light brown sugar
- 65 grams granulated white sugar
- 1 large egg, at room temperature
- 1 teaspoon vanilla extract
- 3 teaspoons water
- additional granulated white sugar for rolling
For the Toasted Marshmallow Cream Frosting
- 1 jar (7 oz/198 grams) Marshmallow Fluff
- 113 grams unsalted butter, room temperature
- 44 grams vegetable shortening
- 227 grams powdered sugar
- ½ teaspoon (2 grams) kosher salt
- 1 teaspoon vanilla extract
- 2 Tablespoons milk, any percentage
For Garnish - optional
- Mini Marshmallow Bits like Jet Puffed Marshmallow Bits
- Chocolate Sprinkles
How to make Gluten Free Chocolate Thumbprint Cookies
- In a medium bowl sift together the gluten-free flour, cocoa powder, baking soda, espresso powder, and salt and set aside.
- In a stand mixer, combine the butter, brown sugar, and granulated sugar and on medium-high speed cream until smooth and creamy, about 4-5 minutes. Scrape down the sides of your bowl.
- Add the egg, vanilla extract, and water and beat on high speed until combined, about 1 minute. Scrape down the sides and up the bottom of the bowl and mix to combine.
- Mix the dry ingredients into the wet ingredients and mix on low until combined. The cookie dough will be thick.
- Use a 1 tablespoon cookie scooper and portion the cookie dough into little portions. Form them into balls and roll each into granulated sugar.
- Place cookie dough balls onto a large lined baking sheet. Using your thumb, make an indent into each cookie. Chill the shaped cookies for at least 2 hours in the refrigerator.
How to bake Gluten Free Chocolate Thumbprint Cookies
- Preheat the oven to 350°F. Line a baking sheet with parchment paper. Remove chilled and shaped cookies from the refrigerator.
- Place 8 cookies on your prepared baking sheets, spacing the cookies about 2-3 inches apart. Bake for 11-13 minutes or until the edges are set.
- Remove from the oven. The indents will have lost some shape or have puffed up, so use the end of a spatula to make an indent again into the warm cookies.
- Allow cookies to cool for 5 minutes before transferring to a wire rack to cool completely before filling with toasted marshmallow cream.
How to make toasted Marshmallow Cream Frosting
Toast Marshmallow Fluff
- Line a sheet tray with foil and lightly spray with nonstick pan spray. Remove the marshmallow fluff from the jar and then spread it evenly on your foil-lined sheet tray.
- With a kitchen torch (or your broiler) toast the marshmallow fluff to your liking.
- Stir your toasted marshmallow creme, allow for it to cool (especially if you put it under the broiler)
Toasted Marshmallow Cream Filling
- In the bowl of your stand mixer fitted with the paddle attachment or a large mixing bowl, combine the room temperature butter and the shortening, and beat until light and fluffy. Make sure to scrape down the sides and the paddle.
- With the mixer on LOW gradually add in the powdered sugar and continue to mix until all the sugar is incorporated. Add in kosher salt, vanilla extract, and milk and mix for one minute. Stop the mixer and scrape down the sides of your bowl and paddle.
- Add the toasted and cooled marshmallow fluff and mix at medium-high speed for 2 minutes.
- If your frosting seems very stiff, add an additional teaspoon of milk. Set the frosting aside (keep at room temperature) until ready to fill your Chocolate Thumbprint Cookies
Fill and Garnish Thumbprint Cookies
When your cookies are fully cooled, fill each indent with the toasted marshmallow frosting. Sprinkle with Mini Marshmallow Bits and Chocolate Sprinkles.
Cookies are the best when enjoyed with 3 days. Store them in a cool room in an airtight container (avoid the fridge if possible)
Amount Per Serving: Calories: 243