Start by preheating your oven to 350 degrees Fahrenheit. Line a 12-cup muffin tin with paper liners or lightly grease with nonstick spray. This step ensures your muffins release easily and maintain their shape.
In a medium bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg. Mixing the dry ingredients first helps to evenly distribute the leavening agents and spices, so every muffin has consistent flavor.
In a large mixing bowl, whisk together melted butter, granulated sugar, brown sugar, eggs, vanilla extract, and yogurt until smooth and creamy. Make sure your butter is not too hot or it can cook the eggs.
Fold in the chopped apples to the wet mixture. The apples add moisture and natural sweetness, giving each muffin a tender and fruity bite. Make sure they are evenly distributed for consistent flavor.
Gently fold the dry ingredients into the wet ingredients using a wooden spoon or spatula. Mix until just combined. Do not overmix or the muffins can turn out dense. It is okay if a few flour streaks remain.
Divide the batter evenly among the prepared muffin cups, filling each about 3/4 full. Bake for 22 to 25 minutes, or until a toothpick inserted in the center comes out clean. Allow muffins to cool in the pan for 5 minutes, then transfer to a cooling rack.