Shred the zucchini on the small holes of a box grater. You should get roughly 3 cups shredded from 14-15 ounces of zucchini. Lay down two layers of paper towels and spread the shredded zucchini onto it. Place two more layers of paper towels across the top and blot it firmly with the palms of your hands until it weighs 9.5 oz (about 1¾ cups packed). Set aside. Blotting to weight is what keeps the crumb from turning gummy.
14 ounces zucchini
In a large bowl, whisk together the flour, cocoa, baking soda, baking powder, salt, and coffee granules.
In a small bowl, toss the 1/2 cup dark chocolate chips with a spoonful of the dry mixture. Coating the chips keeps them from sinking as the muffins bake.
1/2 cup dark chocolate chips
In a medium bowl, whisk together the oil, granulated sugar, brown sugar, eggs, vanilla, and sour cream until smooth and well blended.
Add the wet mixture to the dry and stir just until barely combined; a few flour streaks are fine. Fold in the blotted zucchini, then the floured chips. Do not over mix, or the muffins will turn tough.
Let the batter rest 20 minutes. This hydrates the flour, relaxes the gluten, and thickens the batter for taller crowns, and it lets the flour absorb moisture from the zucchini for a better-set crumb.
Preheat the oven to 425°F during the rest.
Line two muffin pans with paper liners (6 in each pan, not all 12), or butter the wells and dust with cocoa (avoid cooking spray, which can leave a tacky film on the muffins). Divide the batter among 12 cups across the two pans, 6 per pan, so they have room to dome without touching. Sprinkle the tops with the semi-sweet chocolate chips.
1/3 cup semi sweet chocolate chips
Bake at 425°F for 5 minutes to force a fast rise and set the crown. Do not open the oven.
Without opening the oven door, reduce the temperature to 350°F and bake 17 to 20 minutes more, until a toothpick inserted in the center comes out clean or with a few moist crumbs (not wet batter).
Cool the muffins in the pans for 5 minutes, then transfer to a wire rack to cool completely. They finish setting as they cool.
I use natural unsweetened cocoa, but Dutch-process will give you an even darker, smoother result if you like.
There's no need to peel your zucchini first. You won't even be able to tell once they are baked.
You will not taste coffee at all, it just deepens the cocoa. Espresso powder works too, and since it is more concentrated I use about half a teaspoon in its place. If you would rather leave the coffee out entirely, a teaspoon of ground cinnamon is lovely as well!