Preheat your oven to 180°C (350°F). In a bowl, whisk together the all-purpose flour, cocoa powder, and salt until well combined.

In another large mixing bowl, beat together the room-temperature unsalted butter, granulated sugar, and brown sugar until light and fluffy.

Add in the egg yolks one at a time along with the vanilla extract. Mix until fully incorporated.

Gradually add your dry mixture to the wet mixture, mixing just until combined.

Scoop out tablespoon-sized portions of dough and roll them into balls. Place them on a lined baking sheet about two inches apart. Press down in the center of each ball to create an indentation.

Bake in your preheated oven for about 10 minutes until set but still soft in the center.

While your cookies are cooling slightly, prepare your ganache by heating heavy cream in a small saucepan until it just begins to simmer. Remove it from heat and add chopped dark chocolate along with cold unsalted butter. Stir until smooth and glossy.

Once your cookies have cooled completely, fill each thumbprint indentation with chocolate ganache using either a spoon or piping bag.