Preheat oven to 325 degrees F (165 degrees C). Spray 36 mini muffin cups with cooking spray.
Heat a large skillet over medium-high heat and crumble in sausage. Cook and stir until sausage is crumbly and evenly browned, about 10 minutes . Drain and discard any excess grease.
Sprinkle sausage, Cheddar cheese, Swiss cheese, and green onion evenly into the prepared muffin cups.
Beat eggs, potato flakes, and cream together in a bowl; season with salt and pepper. Pour egg mixture evenly over the sausage-cheese mixture in the muffin cups.
Bake in the preheated oven until quiches are set in the middle and lightly browned, about 22 minutes. Cool for 5 minutes before serving.
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