Prep the pan and oven. Heat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease it.
Grate the zucchini. Use the large holes of a box grater. Spread the grated zucchini on a clean towel and gently squeeze out excess moisture. You don’t need it bone-dry—just remove the watery drips.
Mix the dry ingredients. In a large bowl, whisk flour, cocoa powder, baking soda, baking powder, salt, and cinnamon until evenly combined.
Whisk the wet ingredients. In another bowl, whisk eggs, granulated sugar, brown sugar, oil, vanilla, and yogurt until smooth.
Combine wet and dry. Pour the wet mixture into the dry ingredients.
Stir with a spatula until almost combined. A few dry streaks are okay at this stage.
Fold in zucchini and chips. Add the grated zucchini and chocolate chips. Fold gently until the batter is just combined.
Do not overmix.
Fill the muffin cups. Divide the batter evenly among the cups, filling each about 3/4 full. Sprinkle a few extra chocolate chips on top for a bakery look.
Bake. Bake for 18–22 minutes, or until the tops spring back and a toothpick inserted in the center comes out with a few moist crumbs (melted chocolate is fine).
Cool. Let muffins cool in the pan for 5 minutes, then move them to a wire rack to cool completely. This helps set the crumb and keeps the bottoms from getting soggy.