Start by beating the softened salted butter together with the brown sugar and granulated sugar in a large bowl or stand mixer. Mix until it’s light, fluffy, and creamy, you’ll see it change right before your eyes. Don’t forget to scrape down the sides a couple of times so every bit is included. Next, add the egg and vanilla extract and mix until fully incorporated.
In another bowl, whisk the flour, Dutch-process cocoa, and baking soda together. This little step ensures the dough stays smooth and that every bite is packed with even chocolate flavor.
Now, gently fold the dry ingredients into the butter mixture, adding the milk as you go. Mix just until combined, the dough should be thick, slightly sticky, and ready to shape into cookies.
Scoop out tablespoon-sized portions of dough and place them on a lined baking sheet. Press the end of a spoon into the center of each cookie to make a small well, this is where the ganache will sit later.
Chill the cookies in the fridge for 2–3 hours. This helps them keep their shape while baking and makes handling easier.
Preheat your oven to 350°F (175°C). Bake the chilled cookies for 11–13 minutes, until the edges are set but the centers are still soft. If the thumbprints puff up, gently press them down again. Let the cookies cool for a few minutes on the sheet, then transfer to a wire rack to finish cooling.
Start the ganache by putting the dark chocolate into a bowl suitable for heat exposure. Heat the cream until it just starts to simmer, then pour it over the chocolate. Let it sit for a couple of minutes before stirring until smooth and glossy. Add a tiny pinch of sea salt if you want an extra flavor boost. Let the ganache cool slightly, then spoon a bit into each cookie indentation, and then dig in!