Preheat the oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease the cups.
In a large bowl, whisk together the all-purpose flour, granulated sugar, brown sugar, baking powder, baking soda, ground cinnamon, ground nutmeg, and salt until well combined.
In a separate medium bowl, whisk the melted butter, eggs, whole milk, and vanilla extract until smooth.
Pour the wet ingredients into the dry ingredients and gently fold together using a spatula until just combined. Do not overmix; the batter should be slightly lumpy.
Fold in the diced fresh apples evenly throughout the batter.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 22 to 25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the oven and allow them to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.