Preheat the oven to 325°. Lightly coat a muffin tin with non-stick spray. Set aside.
To a small pan, add the chopped apples and water and bring to a boil. Reduce heat and simmer for 10 minutes or until soft, but not mushy.
Drain remaining water from apples and remove about half the apple chunks. Mash the remaining apples with a potato masher. Set aside and let cool while you make the muffin batter.
Add 1/2 teaspoon sugar and 1/8 teaspoon of cinnamon sugar to remaining apples. Stir until apples are full coated in the cinnamon mixture. Set aside.
In a large bowl, mix together grated zucchini, butter, greek yogurt, egg, vanilla, salt, cinnamon, nutmeg, baking soda and sugar. Add cooled mashed apples and stir until fully combined.
Add white and wheat flour and gently fold into zucchini mixture. Be careful not to over-mix.
Fill muffin tins about 3/4’s full of batter. Add a few apple chunks to the top of each muffin, lightly pressing the apples into the batter.
Bake for about 30 minutes or until slightly golden and a toothpick inserted in the center comes out clean.
Remove from oven and cool for 10 minutes. Then remove muffins from pan and place on a cooling rack until room temperature. Store in an airtight container.