Preheat the oven to 375 degrees F. Lightly coat a muffin pan with cooking spray.
In a large bowl, whisk together the whole wheat pastry flour, cinnamon, baking soda and salt.
In a medium bowl, stir together the applesauce, Greek yogurt, brown sugar and egg.
Add the applesauce mixture to the flour mixture and stir well to combine.
Stir in the grated zucchini and carrot, and ⅓ cup chopped pecans.
Divide the batter evenly between the muffin cups (about ¼ cup each).
Bake for 7 minutes. Place the remaining 3 tablespoons pecan pieces on top of the muffins. Bake until a toothpick inserted in the center of the muffins comes out clean, and additional 7 to 9 minutes.
Remove the muffins from the pan and allow to cool. Serve immediately or store in an airtight container.