Add the spinach to a large, heavy skillet and cook, stirring frequently, over medium heat until it's completely thawed and all of the moisture has evaporated. Transfer to a bowl and set aside.
Add the butter to the pan and melt over medium heat. Add the onion and sauté until soft and translucent, 3 to 4 minutes.
Sprinkle the flour over the onion and continue cooking, stirring often, until the mixture turns golden, 4 to 5 minutes.
Warm the milk in the microwave for 1 minute, then slowly add it to the onion mixture. Continue cooking, stirring constantly, until the mixture thickens, 2 to 3 minutes. Season with salt and pepper.
Stir in the reserved spinach along with the cream cheese and combine thoroughly.
Add the sour cream, mix well and continue cooking until the creamed spinach is hot and bubbly, 1 to 2 minutes longer. Season to taste with salt, pepper and nutmeg and transfer to a serving bowl.