Combine flour, baking powder, baking soda, salt, and sugar in a large bowl. Make a well in the center.
Combine milk with lemon juice and let sit for 10 minutes. Add milk mixture to the flour mix along with the eggs, melted butter, lemon zest, and vanilla. Whisk together until the batter is mixed. Let rest for 30 minutes.
Heat waffle maker. Pour about ½ cup of the waffle batter onto the waffle maker. Cook until golden brown and crisp. Repeat with remaining batter. Dust waffles with powdered sugar and serve immediately.