Preheat oven to 350 degrees F. Lightly coat a 13x9x2-inch baking pan with nonstick cooking spray; set aside. In a large bowl, combine all-purpose flour, whole wheat flour, flaxseeds or wheat germ, cocoa powder, baking powder, and salt. Make a well in center of flour mixture; set aside.
In a medium bowl, whisk together egg, sugar, canola oil, and milk until well mixed. Stir in zucchini and banana. Add zucchini mixture all at once to flour mixture. Stir just until moistened. Fold in chocolate pieces. Pour batter into prepared pan, spreading evenly.
Bake about 25 minutes or until top springs back when lightly touched. Cool completely on a wire rack. Cut into squares.