Prep the pan: Preheat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or grease lightly.
Whisk dry ingredients: In a large bowl, whisk the flours, cinnamon, baking powder, baking soda, and salt until well combined.
Mix wet ingredients: In a separate medium bowl, whisk the eggs, Greek yogurt, applesauce, maple syrup, oil, and vanilla until smooth.
Combine gently: Pour the wet ingredients into the dry. Stir with a spatula just until no dry streaks remain. Do not overmix.
If using mix-ins, fold them in now.
Fill the cups: Divide the batter evenly among the 12 muffin cups. The cups should be about 3/4 full. Sprinkle the optional cinnamon sugar on top.
Bake: Bake for 16–20 minutes, or until the tops are set and a toothpick inserted in the center comes out clean or with a few moist crumbs.
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely.
This helps keep the crumb tender.