Preheat your waffle iron according to manufacturer's instructions, allowing at least 5 minutes for it to reach full temperature.
In a large mixing bowl, whisk together the flour, brown sugar, baking powder, baking soda, cinnamon, nutmeg, and salt until the brown sugar is broken up and evenly distributed.
In a separate bowl, whisk the eggs until slightly frothy, then add the milk, melted butter, and vanilla extract. Whisk until fully combined.
Pour the wet ingredients into the dry ingredients and gently fold together with a spatula until just combined. Some small lumps are fine — overmixing will make tough waffles. Let the batter rest for 5 minutes.
Lightly grease the waffle iron if needed. Pour the recommended amount of batter for your iron size (usually 1/2 to 3/4 cup) onto the center of the hot waffle iron.
Close the lid and cook without opening until the steam stops escaping and the waffle is deep golden brown, about 4-5 minutes. The exact time depends on your iron.
Carefully remove the waffle using a fork or silicone tongs and place on a wire rack. Avoid stacking waffles directly on a plate, which traps steam and makes them soggy.
Repeat with remaining batter, keeping finished waffles warm in a 200°F oven on a wire rack set over a baking sheet if desired. Serve immediately with your favorite toppings.