Preheat your oven to 375 degrees F. Grease a 12-cup muffin tin well.
Place the cubed bread evenly into the prepared muffin cups, filling each about two-thirds full.
In a medium bowl, whisk together the eggs, milk, vanilla extract, 1 teaspoon cinnamon, nutmeg, and 1/4 cup granulated sugar until combined.
Pour the egg mixture evenly over the bread cubes in the muffin cups. Press the bread down gently to soak up the liquid. Let stand for 10 minutes.
Prepare the topping: In a small bowl, mix the remaining 1/2 cup sugar, flour, and the remaining ground cinnamon. Stir in the melted butter until the mixture resembles coarse crumbs.
Sprinkle the cinnamon sugar topping generously over the top of each muffin cup.
Bake for 20 to 25 minutes, or until the tops are golden brown and the center is set.
Let the muffins cool in the tin for 5 minutes before carefully removing them to a wire rack to cool slightly.
Notes
Use slightly stale or day-old bread for the best texture; it absorbs the custard better.
You can prepare the batter and soak the bread the night before. Cover the muffin tin and refrigerate. Add 5 minutes to the baking time if baking directly from the refrigerator.
These muffins freeze well. Cool completely, place in an airtight container, and freeze for up to one month. Reheat in the microwave or toaster oven.