Preheat the oven to 325°F. Line baking sheets with parchment paper.
In a medium bowl, whisk together the flour, cocoa powder, baking soda, ginger, cinnamon, salt, cloves, and nutmeg until combined.
In the bowl of an electric mixer fitted with the paddle attachment, beat the butter and fresh ginger on medium speed until fragrant, about 2 minutes. Add the brown sugar and beat until light and fluffy, about 2 to 3 minutes, scraping down the sides and bottom of the bowl as needed.
Add the molasses and beat until combined. Then add the egg and vanilla, beating until very well combined. Scrape down the sides and bottom of the bowl again.
On low speed, gradually add the flour mixture. Stir in three-quarters of the chocolate chips until just combined. Dough will be sticky.
Using a medium spring-loaded scoop, divide the dough into 1 ½-tablespoon-sized scoops.
Place sugar in a shallow dish and roll each scoop in the sugar. Gently form each scoop into circular balls before placing on baking sheets. Dot each scoop with a few chocolate chips.
Bake for 10 minutes, or until the tops are set.
Let cool on the baking sheets for 5 minutes before removing to cooling racks to cool completely. Cookies can be stored in an airtight container at room temperature for up to 3 days.