Preheat oven to 425 degrees. Line a standard muffin tin with paper liners and set aside.
In a large bowl, combine flour, cocoa powder, ginger, cinnamon, nutmeg, cloves, baking soda and salt. Whisk until combined then set aside.
In a separate bowl, beat brown sugar and butter until light and fluffy.
Add eggs, one at a time, beating after each until well combined. Scrape down the sides of the bowl as needed.
Whisk in molasses, milk and yogurt until combined.
Add wet ingredients to dry, gently stirring with a spoon until just combined. There should be flour still visible. Do not overmix.
Fold in chocolate chips then evenly distribute batter among 12 muffin cups.
Bake for 5 minutes at 425 degrees then lower oven temperature to 350 degrees and continue baking for 13 to 15 minutes. Muffins are done when a toothpick inserted in the center of the muffin comes out with a few moist crumbs. Avoid overbaking.
Cool muffins in the tin for 5 minutes before removing to a wire rack to cool completely.
Store muffins in a airtight container at room temperature up to 3 days.