Treat yourself to Gluten-Free Chocolate Thumbprint Cookies with Ganache. These cookies are rich, thick, and fudgy with minimal effort. There is a LOT of chocolate in this recipe, which creates an amazing, slightly chewy texture, and a soft bite with more chocolate in the centre. If you’re craving something sweet with your coffee, these Gluten-Free Chocolate Thumbprint Cookies with Ganache are perfect.
These thumbprint cookies are loaded with chocolate in the dough and in the ganache filling. The dough has basic ingredients that are quick and easy to mix together. After shaping and chilling the cookies, they bake in just 12 minutes, for a very quick and easy cookie recipe. The ganache filling is just as easy! Heat the cream, pour it over the chocolate wafers, stir the two ingredients together.
Ideal cookies for the holidays, gifting, or anytime you want a bakery style chocolate cookie that feels indulgent. In fact, Gluten-Free Chocolate Thumbprint Cookies with Ganache are a must try for any chocolate lover.
Why This Recipe For Gluten-Free Chocolate Thumbprint Cookies with Ganache Works
- A high amount of dark, melted chocolate adds richness and structure. As it cools, it firms up the cookie, helping it stay thick instead of spreading flat.
- Dutch-process cocoa powder deepens the chocolate flavor without adding extra fat, keeping the dough balanced and not greasy.
- An egg to help bind the gluten-free dough
- A mix of granulated and brown sugar gives structure and moisture without excessive spreading.
- Gluten-free 1-to-1 flour blend with xanthan gum provides just enough structure allowing the chocolate to lead the flavor.
- Chilled dough before baking is essential for these cookies. This helps the cookies set and not flatten out too much while baking.
Gluten Free Flours Used For Cookies
GF flour blend – For this recipe, I used a 1-1 Flour blend that includes xanthan gum
For the best results with gluten free baking I prefer to use a kitchen scale. This makes measuring ingredients not only more accurate but also less clean up, when not using all those cups and spoons. Here is the link to the scale that I use.
Baking Tips for Perfect GF Cookies
- Cool the melted chocolate before adding it to the dough. Warm chocolate will melt the butter and cause spreading.
- Use a 3-tablespoon cookie scoop for uniform baking and the perfect ganache to cookie ratio.
- Chill the dough in the freezer for 5 minutes, or in the fridge for 20 minutes before baking to prevent the cookies from spreading flat.
- Press the indent after baking and let the cookies cool.
- Fill with the ganache while it is slightly warm not hot, so it settles smoothly without melting.
- These steps help achieve the ultimate Gluten-Free Chocolate Thumbprint Cookies with Ganache



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Gluten-Free Chocolate Thumbprint Cookies
Ingredients
Cookie Dough
- 200 g dark chocolate chopped
- 150 g gluten-free 1-to-1 flour blend
- 15 g of almond flour
- 20 g unsweetened Dutch cocoa powder
- ½ tsp baking powder
- ¼ tsp salt
- 100 g butter softened (not melted)
- 120 g granulated sugar
- 60 g light brown sugar packed
- 1 large egg
- 1 tsp vanilla extract
Ganache
- 80 g dark chocolate chopped
- 60 ml whipping cream
- crushed candy canes for topping
Instructions
Cookie Dough
- Gently melt the 200 g dark chocolate and let it cool to lukewarm. It should not be hot and melt the butter.
- Preheat the oven to 350 °F and line a baking sheet with parchment paper.
- Whisk together flour, cocoa powder, baking powder, and salt.
- Beat softened butter with sugars until light and fluffy, about 2–3 minutes.
- To the butter mix add the egg and vanilla. Beat until combined and fold in the cooled, melted chocolate.
- Add the dry ingredients, folding them in until just combined and let the dough rest at room temperature for 10 minutes.
- Scoop about 3 Tbsp dough per cookie and roll into balls and place them on the baking sheet spaced 2 inches apart. Don't flatten them.
- Chill the dough balls for 5 to 10 minutes in the freezer. Alternatively leave the dough in the fridge for 20 minutes or overnight.
- Bake for about 12 minutes, until the edges are just set. Do not overbake.
Ganache
- Heat cream until just about simmering but boiling. Pour the hot cream over the chocolate and stir until smooth and let cool slightly.
- Let ganache set at room temperature or refrigerate briefly.
- Once cookies are cooled slightly … but still warm. Gently press a tablespoon sized indent in the top of each cookie and spoon or pour the ganache into the indent.
- Sprinkle crushed candy canes or other sprinkles while the ganache is still warm
- Store in an airtight container for 3-5 days or freeze for unto 2 months
Key Takeaways
- Gluten-Free Chocolate Thumbprint Cookies with Ganache are rich, fudgy, and easy to make, perfect for chocolate lovers.
- The recipe uses melted dark chocolate, cocoa powder, and a gluten-free flour blend, ensuring a chewy texture.
- Chill the cookie dough before baking to prevent spreading and achieve perfect thumbprints.
- Baking tips include cooling chocolate, using a 3-tablespoon scoop, and filling cookies with ganache when warm.
- These cookies are ideal for holidays, gifting, or satisfying sweet cravings with coffee.

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