Preheat oven to 400°F.
Cut pie crust into circles, approximately 3 1/2 inches in diameter. (This can be done with a knife, drinking glass, or round cookie cutter.) Spray muffin pan with cooking spray and then press a dough circle into each cup.
Put a cupcake liner over the top of each crust and fill with the dried beans; this will ensure that the crust does not rise while baking. Bake for 10 minutes, then allow beans to cool and remove the cupcake liners.
While crusts are cooling, whisk together the eggs, milk, nutmeg, and salt.
Dice broccoli and mushrooms into smaller pieces and place them into each of the cooked pie crusts.
Pour in the egg mixture and top with shredded cheese. Bake again for 10-15 minutes. The eggs will rise up and the crust will become slightly golden.
Serve with apple slices on the side.