Cook macaroni according to package instructions, or until al dente. Drain, rinse, and set aside.
In large saucepan, sauté onion in butter for 2 minutes until transparent. Blend in flour, stirring well to incorporate, and cook for an additional minute. Whisk milk into butter and flour mixture. Bring to simmer and cook until sauce thickens.
Reduce to low heat and add pepper and mustard. Stir in 2 1/2 cups of the cheese until blended into the sauce.
Add cooked macaroni and prosciutto to cheese sauce, and mix well. Place macaroni mixture in buttered, oven proof, 9” x 9” dish. Top with remaining 1/2 cup of cheese.