In a medium bowl, beat the eggs with the heavy cream until well combined and a bit frothy.
In a separate bowl, mash the softened cream cheese with a fork until smooth. Add the shredded cheese to the cream cheese and stir to combine; it doesn’t have to be perfect, just mostly mixed.
Stir the cream cheese and shredded cheese mixture into the beaten eggs. Whisk or stir until as smooth as you can get it. A few small bits of cream cheese are fine; they’ll melt into little pockets of richness.
Add the crumbled bacon, chopped spinach, chopped onion or green onion, garlic powder, salt, pepper, and optional red pepper flakes. Stir until everything is evenly distributed.
Divide the mixture evenly among the prepared muffin cups, filling each about 3/4 full. If using, sprinkle a little grated Parmesan over the tops for extra flavor and a light crust.
Bake in the preheated oven for 18–22 minutes, or until the cups are set in the center and lightly golden around the edges. A toothpick inserted in the middle should come out mostly clean.
Remove the muffin tin from the oven and let the cups cool in the pan for about 5–10 minutes. They will puff up in the oven and then settle a bit as they cool—that’s perfectly normal.
Run a small knife around the edges, if needed, and gently lift the cups out. Serve warm, or let them cool completely and refrigerate in an airtight container for up to 4 days.
To reheat, warm in a low oven (300°F/150°C) for 8–10 minutes, or microwave gently in short bursts until heated through.
