In a separate bowl, stir together the flour, cocoa powder, baking soda, cinnamon, and salt. Gradually add the dry ingredients to the wet ingredients, folding by hand with a wooden spoon or spatula until completely blended. The batter will be very thick. Fold in the zucchini and chocolate chips.
Scoop the batter into the prepared muffin cups, evenly filling each cup. Sprinkle the tops of each muffin with more chocolate chips. Bake for 20 to 25 minutes or until the tops are set and a toothpick inserted in the center of the muffin comes out clean with just a few moist crumbs clinging to it. Let the muffins cool in the pan for a few minutes, then transfer to a wire rack to cool completely. Store the muffins in an airtight container, at room temperature.