Mix together the eggs, milk, salt, pepper and flour.
Generously grease two 12-cup muffin tins with nonstick vegetable oil spray. Press crêpes into tins, lightly ruffling edges but being careful not to tear them.
Place a small square of cheese into bottom of each crêpe and pour egg mixture carefully over it, filling just to below top of rim. Top with crumbled turkey bacon.
Bake crêpes at 375°F until mixture is firm and crêpes are just lightly browned, about 15 to 20 minutes. Let cool slightly and carefully loosen crêpe cups from muffin tins with a fork or knife, taking care not to break crêpe edges. Remove from tins with a spoon.