Prep your pan and oven. Heat the oven to 400°F (200°C). Line a 12-cup muffin tin with paper liners or grease lightly.
Mix the dry ingredients. In a large bowl, whisk wholemeal flour, baking powder, baking soda, salt, 2 teaspoons cinnamon, and brown sugar until no lumps of sugar remain.
Grate the apples. Peel and grate the apples on the large holes of a box grater. Toss with lemon juice if using. Lightly squeeze by hand to remove only excess drip, not all moisture.
Combine the wet ingredients. In a separate bowl or large measuring jug, whisk eggs, yogurt, milk, oil, honey (or maple), and vanilla until smooth.
Bring the batter together. Pour wet ingredients into the dry. Add the grated apples and any mix-ins (nuts, raisins). Stir with a spatula just until combined. Do not overmix; a few streaks of flour are fine.
Fill the muffin cups. Divide the batter evenly among the 12 cups. They should be quite full, about 3/4 to almost to the top.
Add the topping. Mix a pinch of cinnamon with turbinado sugar and sprinkle over each muffin for a crisp lid.
Bake hot, then lower. Bake at 400°F (200°C) for 5 minutes to help lift the domes. Without opening the oven, reduce heat to 350°F (175°C) and bake another 12–15 minutes, until a toothpick comes out with a few moist crumbs.
Cool correctly. Let muffins rest in the pan for 5 minutes, then move to a wire rack. This keeps bottoms from steaming and getting soggy.
Enjoy warm or at room temp. They’re lovely as is or split and spread with a little butter or almond butter.