In a large saute pan, melt the butter over medium heat. Add the onions and saute until translucent, about 15 minutes. Stir in the flour and nutmeg and cook for about 2 minutes stirring constantly so the flour does not burn. Pour in the cream and milk and cook until thickened.
Working in batches, add the kale once cup at a time to the cream sauce and stir until wilted. Add 1 cup of Parmesan cheese, 1/2 cup of Gruyere and stir thoroughly. Stir in the salt and pepper and remove from the heat.
Transfer the spinach mixture to a baking dish and sprinkle the remaining cheese over top evenly. Bake for 20 minutes or until hot and bubbling. Serve immediately.