Preheat the oven to 350 degrees F. Line a 12-cup muffin pan with paper liners.

In a medium bowl, stir together both flours, baking powder, cinnamon and salt. In a large bowl, whisk together the eggs, oil, applesauce, sugar, zucchini and vanilla extract. Fold the dry ingredients into the wet ingredients followed by 1/2 cup bittersweet chocolate. Transfer the batter the prepared muffin pan and sprinkle with the remaining chocolate.

Bake the muffins for 22-25 minutes until the tops spring back when pressed. Cool in the pan for 5 minutes before removing the muffins and transferring them to a wire rack to cool completely.

Store in an airtight container.