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In a medium mixing bowl combine flour, unsweetened cocoa, ground ginger, cinnamon, cloves, and nutmeg. Set aside.
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Ina large bowl, beat together butter, brown sugar, and fresh ginger until fluffy, about 1 minute. Add molasses, and mix until completely incorporated, scraping sides of bowl as needed.
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Add flour mixture to butter mixture in two additions, mixing until just combined after each addition.
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Fold in chocolate chips and crystallized ginger by hand.
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Refrigerate cookie dough for at least one hour, to overnight.
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Preheat oven to 350 degrees F. Line a baking sheet with a Sil-Pat or parchment paper.
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Place about 1/3 cup sugar in a small bowl.
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Scoop dough by the heaping tablespoon full (or use a small cookie scoop) and then roll each scoop into a ball with your hands. Roll each dough ball in sugar until completely coated. Place on prepared baking sheet about 1 1/2-inches apart.
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Bake for 10 to 12 minutes, or until cookies are cracked on top and firm around the edges. {My cookies looked like a ball until the last 2 to 3 minutes of baking, don't worry if yours do the same.}
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Remove from oven and allow to cool on pan for 5 minutes. Then transfer to a wire rack to cool completely.