Bring a large pot of lightly salted water to a boil. Cook linguine at a boil until tender yet firm to the bite, about 11 minutes. Drain, reserving about 1 cup pasta water.

Melt butter in a saucepan over medium heat. Add mushrooms, onion, and garlic; cook until soft, about 5 minutes.

Increase heat to medium-high; cook and stir until mixture reaches a simmer. Stir in flour, stirring constantly, until no lumps remain. Season with salt and black pepper.

Stir in cream, then cheese and nutmeg, stirring constantly. Reduce heat to medium-low; simmer until thickened, stirring every 5 minutes to prevent lumps and sticking.