Prep the pan: Heat the oven to 375°F (190°C).
Line a 12-cup muffin tin with paper liners or grease lightly.
Whisk wet ingredients: In a large bowl, whisk eggs, oil, applesauce, vanilla, and lemon zest until smooth and glossy.
Combine dry ingredients: In a separate bowl, whisk all-purpose flour, whole-wheat pastry flour, baking powder, baking soda, cinnamon, nutmeg, and salt.
Fold together: Add the dry mixture to the wet. Stir gently with a spatula until just combined. If the batter seems very thick, stir in 2–3 tablespoons milk.
Do not overmix.
Add apples: Fold in the chopped apples until evenly distributed. The batter should be thick but spoonable.
Fill the cups: Divide the batter among the muffin wells, filling each about 3/4 full. Sprinkle optional toppings if desired.
Bake: Place on the center rack and bake 16–20 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs.
Cool: Let muffins cool in the pan 5 minutes, then transfer to a rack.
Cool at least 10 more minutes before eating for the best texture.