Preheat the oven to 350°F and grease a 9-inch deep-dish pie plate.
Cook the bacon in a skillet over medium heat until crisp, about 8 minutes. Transfer it to a paper towel-lined plate, leaving about 1 tablespoon of drippings in the pan. Add the shallot and cook for 2 to 3 minutes until soft.
Add the eggs, cottage cheese, milk, flour, salt, pepper and nutmeg to a blender. Blend until completely smooth. Blending the cottage cheese is what gives this quiche its silky, custard-like texture.
Scatter the bacon, shallot and gruyere evenly over the bottom of the pie plate. Pour the egg mixture over the top, then sprinkle with parmesan and chives.
Bake for 35 to 40 minutes, until the quiche is puffed and golden and the center only jiggles slightly when you move the dish.
Let the quiche rest for 10 minutes before slicing so it sets into clean, creamy wedges.