Preheat oven to 350 degrees F (175 degrees C). Spray 2 mini muffin tins with cooking spray.
Melt chocolate squares in a large microwave-safe glass or ceramic bowl in 15-second intervals, stirring after each melting, about 1 minute. Stir in zucchini, applesauce, egg substitute, and vanilla extract; beat well until combined.
Mix sugar, all-purpose flour, whole wheat flour, baking soda, baking powder, cinnamon, and salt together in a large bowl. Add chocolate mixture; stir just until combined. Fold chocolate chips into the batter.
Scoop batter into prepared muffin tins.
Bake in the preheated oven until a toothpick inserted into the center of a muffin comes out clean, about 15 minutes.