Wash spinach, and drain, but do not dry. Transfer to a large skillet. Cover, and cook over medium-high heat, stirring once, until wilted, about 3 minutes. Drain. Let cool slightly; squeeze out any excess liquid. Finely chop; set aside.
Bring a medium saucepan of water to a boil. Add onions, and cook until skins soften, about 3 minutes. Remove with a slotted spoon (reserve water in pan); rinse under cold water. Trim root ends, and remove skins; halve if large. Return water to a boil. Add onions, and cook until tender, about 10 minutes. Drain, and rinse under cold water.
Melt 1/4 cup butter in a medium saucepan over medium heat. Add flour; cook, whisking, 5 minutes. Add milk in a slow, steady stream, whisking constantly. Boil, whisking, 1 minute. Remove from heat.
Melt remaining tablespoon butter in a large saucepan over medium-high heat. Add bacon; cook, stirring occasionally, until well browned, about 6 minutes. Stir in onions and spinach. Stir in cream and reserved milk mixture. Add 1 teaspoon salt, 1/4 teaspoon pepper, and the nutmeg. Reduce heat to medium-low; cook, stirring, until thickened, about 10 minutes (do not boil). Stir in lemon juice. Season with salt and pepper.
Can be refrigerated in an airtight container up to 2 days; reheat in an oven heated to 300 degrees to serve.