Preheat your oven to 350 degrees f. and line a muffin-tin with cupcake liners. I really like my reusable silicone liners for these, because they don't stick.
Thoroughly wash your zucchini and trim off the ends.
Using a hand grater, grate your zucchini.
Next using your clean hands, squeeze the grated zucchini lightly, over a bowl to remove any excess moisture.
In a large bowl, whisk together both flours, cacao powder, baking powder, baking soda, and sea salt.
In another mixing bowl, beat the eggs until pale and frothy.
Add in the yogurt, maple syrup, applesauce, and vanilla extract.
Gently fold in your dry ingredients and whisk until combined.
Add in shredded zucchini and chocolate chips; fold again.
Ladle your batter equally among the muffin cups, and top with a few more chocolate chips if desired.
Bake for 18-20 minutes or until a toothpick inserted into the center comes out clean.
Once done, remove from the oven and allow to cool at room temperature for about 10 minutes.
Serve warm and enjoy.
You can store your muffins in an airtight container at room temperature for up to 5 days, or freeze in a zip-lock bag for up to 2 months.