Preheat oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease lightly.
In a large bowl, whisk together flour, baking powder, baking soda, salt, cinnamon, nutmeg, granulated sugar, and brown sugar.
In another bowl, whisk melted butter, eggs, milk, yogurt, and vanilla extract until smooth.
Pour wet ingredients into dry ingredients. Mix gently until just combined. Do not overmix.
Fold diced apples into the batter evenly.
Divide batter evenly, filling each cup about ¾ full.
Sprinkle cinnamon sugar topping over each muffin. Bake 18–22 minutes until golden and a toothpick inserted comes out clean.
Let muffins cool for 5 minutes before transferring to a wire rack.