In the medium bowl, whisk together the whole wheat flour, white flour, baking powder, baking soda, salt, and nutmeg. Set aside.
In the bowl of the stand mixer, cream together the butter and sugar until it’s light and fluffy. Scrape down the bowl and add the eggs one at a time, beating after each. Add the vanilla and Greek yogurt and mix until it’s all well combined, then stir in the grated zucchini.
Add the dry ingredients, about a cup at a time, mixing on low just until the batter is smooth. Cover the bowl and refrigerate for at least one hour. (The refrigeration time helps the whole wheat flour to absorb the liquids.)
Preheat the oven to 400° F/200° C.
Scoop the chilled batter into the prepared pan/muffin cups and sprinkle with a little cinnamon sugar. Bake until the muffins are cooked through and a tester comes out clean, about 22 to 26 minutes. Remove from the oven and allow the muffins to cool in the pan for 5 minutes, then turn them out on a rack to finish cooling.