Preheat the oven to 425 degrees F. Line a 12-muffin tin with cupcake liners and set aside.
Whisk the flour, sugar, baking powder, salt, and nutmeg together in a medium bowl; set aside.
Put the butter in a microwaveable-safe dish or measuring cup. Cover with plastic wrap and microwave until melted, about 30 seconds. (Alternatively melt the butter in a saucepan.) Whisk the milk, eggs, lemon zest, and vanilla with the butter.
Make a small well in the center of the dry ingredients. Pour wet ingredients into the well, then stir with a wooden spoon until the dry ingredients are moistened but still lumpy. Do not overmix the batter or your muffins will be dense. Gently stir in the blueberries. Divide the batter evenly into the muffin tin and sprinkle the tops generously with sugar.
Put the muffins in the oven and immediately reduce oven temperature to 375 degrees F. Bake until golden brown, about 25 minutes, rotating the pan halfway through the cooking. (Insert a toothpick into the center of a muffin to check if it is done. Toothpick should come out clean). Cool muffins in the pan on a rack for a couple minutes. Turn the muffins out of the pan and cool on the rack. Serve warm or at room temperature.
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