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Preheat the oven to 350 degrees, and line two baking sheets with parchment paper or a non-stick sheet.
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In a medium bowl, whisk together the flour, cocoa powder, baking soda, baking powder, salt, 1 tsp. cinnamon, ginger, cloves. Set aside. In a large bowl, beat together the melted butter, brown sugar, and 3/4 cup sugar. Mix in the vanilla extract, egg, egg yolk, and coffee. Slowly add in the flour mixture, and stir until completely combined.
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Scoop rounded tablespoonfuls of the dough into your hands, and roll into a ball. In a small bowl, stir together the remaining 1/4 cup sugar and 1 tsp. cinnamon. Roll the cookies in the cinnamon/sugar mixture. Place on your baking sheet, and press down each dough ball slightly with the bottom of a glass.
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Bake for 8-10 minutes, or until the cookies are set and have cracks on the edges and top. You want to lean on the side of under baking here. Let the cookies cool on your pan before transferring to a wire rack. Optionally, melt the chocolate in a small bowl, and dip each cookie into the chocolate. Allow the chocolate to set before storing. Enjoy!