Preheat the oven to 350F. Prepare your 12-muffin tin by spraying it with non-stick spray or lining it with cupcake liners.
Shred the zucchini until you have a cup and a half. Add the shredded zucchini to a large bowl, along with 2 eggs (at room temperature), Greek yogurt, vanilla extract, sugar and vegetable oil. Whisk together until fully combined.
Sift the all-purpose flour, wheat flour, cocoa powder, salt and baking powder into the bowl of wet ingredients. Whisk just until combined. (Overmixing will lead to a dense muffin.)
Fold in the chocolate chips and pour the batter into the prepared tins. Bake for 18-20 minutes, until a toothpick comes out clean.
Enjoy! Muffins can be stored at room temperature in an airtight container for up to 5 days.