Prepare pasta according to package directions; drain.
Heat butter in a large saucepan over medium heat. Add flour and stir until blended; cook about 3 minutes, just until mixture starts to turn golden.
Whisk in milk. Simmer, stirring often, until thickened, about 7 minutes. Add mozzarella, nutmeg, salt and pepper; let cheese melt and whisk together. Add peas, ham and penne; toss to coat and cook to heat through. Serve with freshly ground black pepper to taste.