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Gluten-Free Chocolate
Thumbprint Cookies

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These lovely gluten-free cookies are perfect treat with a glass of milk or cup of coffee. Made from a combination of flours, all gluten-free and with small amount of sugar, these cookies are also healthy bite.

Try also our gluten-free cookies topped with orange marmalade.

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What you'll need for gluten-free chocolate thumbprint cookies

These cookies have soft texture thanks to the combination of three gluten-free flours we used in this recipe. We combined chestnut, millet and almond flours.

We used chestnut flour which adds nuttiness and great brown colour to the cookies. Millet flour is another great gluten-free flour, finely ground and has similar texture to wheat flour. Almond flour gives fluffy texture and great flavour.

When you pair all this with rich chocolate ganache, the result are amazingly delicious cookies. For additional flavour we added grated orange zest and a dash of Amaretto liqueur.

Making the dough

This recipe start with sifting the chestnut flour, which compress into lumps and need to be sifted to become airy. Once sifted, combine the chestnut flour with millet and almond flours, baking powder and a pinch of salt in one bowl. 

Beat with electric mixer butter and demerara sugar until creamy then add an egg which gives consistency, and Amaretto liqueur and finely grated orange zest to add some extra flavours to the cookies.

Continue to beat for a few minutes then fold the flours gradually, mixing on a low speed. The dough will be soft and sticky so be sure to cool it in the fridge for about 30 minutes to set and harden.

Baking the cookies

Now it's time for shaping the cookies. Scoop a full teaspoon of dough and roll into balls. Place them on the baking sheet lined with baking paper and press your thumb (or handle of a large wooden spoon) into the centre of each balls to make an indentation.

Bake the cookies for about 8-10 minutes then make the indentation in the cookies again, as they will puff up and loose the indent. Leave cookies on the tray until you prepare chocolate filling.

Useful tip

Most thumbprint cookies are baked with the filling inside, but these cookies are baked without filling. Since the cookies are empty, they're going to puff up in the oven and lose some of indentation.

So when cookies come out from the oven, grab the wooden spoon and press the center of the warm cookies down to make a deeper indent. This way you will have room for more delicious
chocolate ganache.

Making the chocolate filling

For the chocolate filling, chop finely dark chocolate on a cutting board. The best tool for this is a serrated knife. Place chocolate in a heatproof bowl.

Heat the whipping cream on a low heat until it just start to simmer and pour it over chocolate. Leave for 1 minute then stir until completely melted. Leave to cool for 5 minutes then fill each indent using a teaspoon. Chocolate ganache will set on the cookies but will still be creamy and delicious.

A few of our favourite gluten-free recipes:

Gluten-Free Chocolate Thumbprint Cookies

MAKES: 24 cookies
COOKS IN: 30 minutes


For the cookies

  • 90g chestnut flour (1 cup)
  • 80g millet flour (1/2 cup + 1 tbsp)
  • 64g almond flour (2/3 cup)
  • 1 teaspoon baking powder
  • 1 pinch of salt
  • 112g butter (8 tbsp), at room temperature
  • 65g demerara sugar (1/3 cup)
  • 1 egg, at room temperature
  • 1 teaspoon Amaretto liqueur
  • 1 tablespoon grated orange zest

For the filling

  • 100g dark chocolate 55-65% (3.5 ounces)
  • 30ml whipping cream 33-36% milk fat (1/8 cup)


  1. FOR THE COOKIES, preheat the oven to 175°C/347°F, 10 minutes before baking. Line the baking sheet with baking paper.

  2. Sift the chestnut flour and combine with millet and almond flours, baking soda and salt in medium bowl.

  3. Place butter and demerara sugar in one bowl and beat with electric hand mixer for about 2-3 minutes or until creamy. Add egg and Amaretto liqueur and continue to beat for a few minutes on a high speed.

  4. Gradually add flours, mixing with hand mixer until just incorporated. The dough is sticky and soft.

  5. Scoop a full teaspoon-sized balls of dough and roll them into 2-cm balls then place them on prepared baking sheet. Leave some space between balls as they will spread during the baking. Using you thumb, gently press an indentation in the centre of each ball.

  6. Bake in the preheated oven for about 10-12 minutes. The cookies will still look soft. Remove from the oven. The indents will loose some shape as the cookies will puff up, so gently press again your thumb into the warm cookies. Allow cookies to cool on the baking sheet for 5-6 minutes, then transfer to a wire rack to cool completely.

  7. FOR THE CHOCOLATE GANACHE, place chopped chocolate into a heat-proof bowl. Heat the whipping cream on a low heat until it start to simmer. Pour over chocolate and let it sit for about 2-3 minutes. Slowly stir the chocolate until completely melted. Cool for at least 10 minutes before filling the cookies.

  8. Fill 1 teaspoon of chocolate ganache to each indentation, going back to add more to those that don't have as much as chocolate as others. Ganache will thicken inside the cookies and set on the tops after a few hours, but will still be creamy when you bite into the cookies.

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