In a medium bowl, whisk together the gluten-free flour, cocoa powder, salt, and baking powder until fully combined. Set aside.

In a large bowl or stand mixer fitted with a paddle attachment, beat the softened butter, brown sugar, and granulated sugar on medium speed for 2–3 minutes, until light, fluffy, and creamy. Scrape down the sides as needed.

Add the egg yolks and vanilla extract. Beat for another 1–2 minutes, until the mixture looks pale, smooth, and well incorporated.

With the mixer on low speed, gradually add the dry ingredients. Mix just until a thick, soft dough forms. The dough should be scoopable but not sticky.

Using a 1-tablespoon cookie scoop, scoop dough and roll gently into small balls. Place on a parchment paper lined cookie sheet, spacing cookies about 2 inches apart.

Use a ¼-teaspoon measuring spoon (or the back of a rounded spoon) to gently press an indentation into the center of each cookie.

Refrigerate the shaped cookies for 1 hour. This helps prevent spreading and keeps the thumbprints defined.

While the dough chills, place chocolate chips in a heat-safe small bowl. Heat the heavy cream in a small saucepan (or microwave) until just beginning to simmer—do not boil.

Pour the hot cream over the chocolate chips. Let sit for 2–3 minutes, then stir until smooth and glossy. Stir in vanilla. Set aside to cool and thicken slightly.

Preheat oven to 350°F (175°C). Bake chilled cookies for 10 minutes on a parchment-lined baking sheet, until the edges are set and the centers look slightly soft.

Immediately after removing from the oven, gently press the centers again if they’ve puffed up.

Optional: Use a small biscuit cutter or round cookie cutter to gently “swirl” around each cookie for perfectly round edges.

Let cookies cool on the baking sheet for 5 minutes, then transfer to a cooling rack to cool completely before filling.

Spoon or pipe the ganache into the center of each cookie.