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Tomato Basil Macaroni and Cheese being scooped up

Tomato Basil Macaroni and Cheese

  • Author: Lindsay
  • Prep Time: 35 minutes
  • Cook Time: 25 minutes
  • Total Time: 1 hour
  • Yield: 10-12 servings
  • Category: Side dish
  • Method: Oven
  • Cuisine: American


This homemade Tomato Basil Macaroni and Cheese is made with a wonderful combination of white cheddar and fontina cheese! It’s a healthier spin on macaroni and cheese that packs LOADS of flavor!


  • 1 pound dry short whole wheat pasta, such as shells, penne, rigatoni or elbows
  • 3 tbsp unsalted butter
  • 1/2 small yellow onion (about 1/2 cup)
  • 4 cloves garlic, minced (about 4 tsp)
  • 1/2 cup white whole wheat flour
  • 4 cups nonfat milk
  • 1 1/2 tsp salt
  • 1/2 tsp ground black pepper
  • 1/4 tsp cayenne pepper, plus additional to taste
  • 3/4 cup nonfat plain Greek yogurt
  • 1 1/2 cups shredded melty cheese (about 6 oz), such as white sharp cheddar, fontina or mozzarella*
  • 1/2 cup shredded parmesan cheese (about 2 oz)
  • 1/2 cup thinly sliced fresh basil, divided
  • 4 small plum tomatoes, cut into thin, round slices



  1. Bring a large pot of salted water to a boil. Add the pasta and cook according to the package directions until barely al dente. Drain and set aside.
  2. Place racks in the center and upper third of your oven and preheat to 350 degrees F. Coat a 9×13 inch casserole dish or similar 3 to 3 1/2 quart dish with nonstick spray.
  3. While the pasta cooks: In a Dutch oven or similar large, heavy-bottomed pot, heat the butter over medium heat. Once melted, add the onion and cook until the onion is fragrant and beginning to soften but is not yet brown, about 2 minutes. Add the garlic, the sprinkle the flour over the top. With a whisk, stir continually until the flour turns golden brown and the white bits disappear, about 1 minute. The flour will be lumpy at first, but will smooth out as you continue with the recipe.
  4. Pour in the milk a few splashes at a time, whisking constantly to break up any lumps. Bring to a simmer and cook, stirring often, until the sauce thickens, 5 to 7 minutes.
  5. Remove the pot from the heat and stir the salt, pepper and cayenne pepper. Let the mixture cool for 1 minute, then stir in the Greek yogurt and melty cheese. Add the drained pasta and half of the sliced basil. With a large spoon or spatula, stir and fold gently to combine the ingredients and coat each piece of the pasta with the sauce. Taste and add additional salt, pepper or cayenne pepper to taste.
  6. Transfer the mixture to the prepared dish. Sprinkle the parmesan over the top. Arrange the sliced tomato on top, overlapping slightly if needed. Bake on the center rack until hot and bubbly, 15-20 minutes. If you’d like a crispy top, turn the oven to broil and transfer the dish to the upper rack. Broil for 2-3 minutes, until the top if as dark golden and crispy as you like, watching it carefully so that it doesn’t burn. Let rest for 5 minutes, the sprinkle on remaining basil and serve hot.
  7.  Refrigerate leftovers in an airtight container for up to 4 days. Reheat individual servings gently in the microwave with a splash of milk to keep them from drying out, stirring periodically.


If using mozzarella cheese, incorporating some cheddar is recommended since mozzarella is quite mild.

To freeze: Use a freezer-safe casserole dish. Instead of baking in step 6, let the mixture cool in the dish completely, the cover tightly and freeze for up to 3 months. Let thaw overnight in the refrigerator. Unwrap, loosely cover with foil, then reheat in a 350 degree oven until heated through, 30-45 minutes.


  • Serving Size: 1 serving
  • Calories: 265
  • Sugar: 5.1 g
  • Sodium: 556.8 mg
  • Fat: 7.7 g
  • Carbohydrates: 36.6 g
  • Protein: 14.8 g
  • Cholesterol: 19.4 mg

Keywords: tomato basil macaroni and cheese, oven baked mac and cheese, easy mac and cheese, homemade mac and cheese