Preheat the oven to 350°F (175°C). In a mixing bowl, combine the butter, dark brown sugar, and granulated sugar. Beat until the mixture is light and fluffy.
Incorporate wet ingredients
Add the eggs, vanilla extract, and instant coffee. Beat until thoroughly combined and smooth.
Add dry ingredients
Gradually mix in the flour, cocoa powder, and baking soda. Stir until just combined, avoiding overmixing.
Shape and coat the dough
Using a small scoop or spoon, portion one tablespoon of dough and roll it into a ball. Coat each ball in granulated sugar and arrange on a parchment-lined baking sheet. Using your thumb, gently press an indent into the center of each dough ball.
Bake the cookies
Bake for 8–10 minutes, or until the tops are crinkled and the centers are set but soft. Remove from the oven and allow them to cool slightly on the tray.
Prepare the ganache
In a microwave-safe bowl, combine the heavy cream and chocolate chips. Heat in 30-second intervals, stirring between each, until the chocolate is fully melted and smooth.
Fill and finish
Spoon the ganache into the thumbprint indent of each cookie. Allow to cool until the ganache sets before serving.
Notes
To make Dark Mocha Crinkle Cookies gluten free, substitute the all-purpose flour with a certified gluten-free baking blend. Confirm that the instant coffee and chocolate chips are labeled gluten free, as some brands may contain additives.