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Melt 2 tablespoons butter in a large skillet over medium heat. Add onion, celery and thyme; cook, stirring, until vegetables are softened, about 4 minutes. Add flour and cook, stirring constantly, until flour is golden, about 4 minutes. Add milk in a slow stream, whisking constantly. Cook until thickened and reduced to 1 1/2 cups, about 4 minutes. Remove pan from heat; whisk in Cheddar and fontina cheeses and nutmeg.
Meanwhile, bring a large pot of salted water to a boil. Stir in pasta; cook until al dente, about 7 minutes. Drain pasta and return to pot. Gently stir together pasta, cheese mixture and salt and pepper. Spoon into eight 5- to 8-ounce ovenproof dishes.
Heat oven to 350°F. Melt the remaining 2 tablespoons butter in a nonstick skillet over medium heat. Add breadcrumbs and cook, stirring, until golden, about 3 minutes. Transfer to a bowl. Sprinkle tops of macaroni and cheese with crumbs. Bake on a cookie sheet on the middle rack until hot and crumbs are golden brown, about 20 minutes.