Place flour, milk, butter, eggs, salt, and pepper into a mixing bowl and whisk together.
Lightly grease each popover insert and fill each well about ⅓ way with batter. Add 1 tablespoon of ham and ½ ounce shredded cheese to each well and top with 1 ½ tablespoons batter.
Place popover pan into oven and bake for 20 to 25 minutes or until popovers have puffed up and are golden brown.
Remove from oven, cool for 1 or 2 minutes and serve.