Bring a large pot of salted water to a boil. Add the spinach and cook for about 1 minute until it begins to wilt. Place into a bowl of cold water to stop the cooking immediately. Drain.
Heat up butter in a 12-inch skillet over medium heat until it melts.
Add the onion and garlic to the skillet and stir occasionally while cooking for 2 to 3 minutes until the onion is soft and translucent.
Add the flour to the skillet and stir constantly while cooking for about a minute until it becomes foamy.
Gradually whisk in the half and half and milk. Add the nutmeg, red chili flakes, salt, and pepper into the skillet. Bring the mixture to a boil, then lower the heat and let it simmer for 5 minutes until it slightly thickens.
Add the spinach and Parmesan cheese into the skillet and mix them in. Cook the mixture for another minute to heat everything through.