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Preheat oven to 375°F. Bring a large pot of lightly salted water to a boil. Add macaroni and cook 8 minutes or according to package directions. Drain and return to pot.
Meanwhile, melt butter in a saucepan over medium heat. Add flour and cook 1 minute. Whisk in milk in a thin stream. Whisk in mustard, onion powder, salt, pepper, nutmeg and cayenne. Bring to a simmer; cook 3 minutes, whisking occasionally.
Remove from heat and whisk in American cheese and 1 cup Cheddar cheese. Whisk a little of the cheese sauce into the egg to temper. Whisk egg mixture back into cheese sauce.
Stir sauce into macaroni. Coat 16 standard muffin cups with cooking spray. Divide macaroni among prepared cups. Top each with 1 tablespoon of the remaining Cheddar cheese. Bake for 18 minutes until lightly browned. Cool slightly before running a thin spatula around edge and spooning out of pans.