Preheat an oven and prepare the muffin tin. Place a rack in the center of the oven, then preheat to 375 F. Line or grease a standard muffin tin.
Mix the dry ingredients. In a large mixing bowl, whisk together 2 cups all-purpose flour, ⅓ cup cocoa powder, ¾ tsp baking soda, ½ tsp baking powder, and ½ tsp Kosher salt.
Mix the wet ingredients. In a separate mixing bowl, whisk together ⅔ cup canola oil, ⅓ cup Greek yogurt, ⅔ cup brown sugar, ½ cup granulated sugar, 2 large eggs, and 2 tsp vanilla extract. Fold in the grated zucchini.
Fold together. Pour the dry ingredients on top of the wet ingredients, then use a rubber spatula to stir until just combined and only a few streaks of flour remain. Fold in 1¼ cup mini chocolate chips, gently mixing to combine.
Bake the chocolate zucchini muffins. Divide the chocolate zucchini batter into the prepared muffin tins about ¾ of the way full. It can be helpful to use a cookie scoop for this. Sprinkle about 1 tsp mini chocolate chips on each muffin. Bake for 18-20 minutes, or until a toothpick or cake tester inserted into the center comes out clean. Repeat with remaining batter.
Cool slightly then serve. Allow the muffins to cool for ~5 minutes then transfer to a cooling rack. Sprinkle each muffin with a pinch of flaky sea salt, if using, then allow to cool completely. Enjoy!