Tomato Basil Macaroni and Cheese Recipe
Introduction
This Tomato Basil Macaroni and Cheese offers a fresh twist on the classic comfort food by combining creamy cheese sauce with bright tomatoes and fragrant basil. It’s a satisfying and flavorful dish perfect for cozy dinners or family gatherings.

Ingredients
- 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
Instructions
- Step 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.
- Step 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.
- Step 3: While the pasta cooks, heat the butter over medium heat in a large heavy-bottomed pot. Add the onion and cook until fragrant and beginning to soften, about 2 minutes. Add the garlic, then sprinkle the flour over the top. Whisk continually until the flour turns golden brown and smooths out, about 1 minute.
- Step 4: Gradually pour in the milk, whisking constantly to break up lumps. Bring to a simmer and cook, stirring often, until the sauce thickens, 5 to 7 minutes.
- Step 5: Remove from heat and stir in salt, black pepper, and cayenne pepper. Cool for 1 minute, then stir in the Greek yogurt and shredded melty cheese. Add the drained pasta and half the basil, folding gently to coat the pasta with sauce. Adjust seasoning as needed.
- Step 6: Transfer the mixture to the prepared dish. Sprinkle parmesan cheese on top. Arrange tomato slices on top, slightly overlapping. Bake on the center rack until hot and bubbly, 15-20 minutes. For a crispy top, broil on the upper rack for 2-3 minutes, watching carefully to prevent burning. Let rest for 5 minutes, then sprinkle remaining basil and serve hot.
- Step 7: Refrigerate leftovers in an airtight container for up to 4 days. Reheat individual servings gently in the microwave with a splash of milk, stirring periodically to prevent drying out.
Tips & Variations
- Substitute the whole wheat pasta with gluten-free pasta if needed for dietary preferences.
- Try adding sautéed mushrooms or roasted red peppers for extra flavor and texture.
- Use a mix of cheeses like sharp cheddar and mozzarella for a richer cheesy sauce.
- For a creamier sauce, replace part of the milk with half-and-half or cream.
Storage
Store leftovers covered in an airtight container in the refrigerator for up to 4 days. Reheat gently in the microwave with a splash of milk, stirring occasionally to keep the sauce creamy and prevent the pasta from drying out.
How to Serve

Serve this delicious recipe with your favorite sides.
FAQs
Can I use regular pasta instead of whole wheat?
Yes, regular pasta works well in this recipe. Whole wheat pasta adds extra fiber and nuttiness, but use your preferred type based on taste and dietary needs.
How can I make this recipe vegan?
To make a vegan version, substitute the butter with plant-based margarine, use a dairy-free milk alternative, replace the Greek yogurt with a plant-based yogurt, and use vegan cheeses or nutritional yeast for flavor.
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Tomato Basil Macaroni and Cheese Recipe
- Total Time: 50 minutes
- Yield: 6 to 8 servings 1x
- Diet: Low Fat
Description
Tomato Basil Macaroni and Cheese is a wholesome twist on the classic comfort food, featuring whole wheat pasta, a creamy cheese sauce enriched with Greek yogurt, and fresh tomato and basil toppings. This recipe delivers rich flavors and a satisfying texture while incorporating whole grains and fresh ingredients for a balanced, cozy meal.
Ingredients
Pasta
- 1 pound dry short whole wheat pasta (shells, penne, rigatoni, or elbows)
Cheese Sauce
- 3 tbsp unsalted butter
- 1/2 small yellow onion (about 1/2 cup), finely chopped
- 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)
Garnish
- 1/2 cup thinly sliced fresh basil, divided
- 4 small plum tomatoes, cut into thin, round slices
Instructions
- Cook Pasta: Bring a large pot of salted water to a boil. Add the whole wheat pasta and cook according to package directions until just barely al dente. Drain well and set aside for later use.
- Preheat Oven and Prepare Dish: Position oven racks in the center and upper third of the oven and preheat it to 350°F (175°C). Lightly coat a 9×13 inch casserole dish or a similar 3 to 3 1/2 quart baking dish with nonstick spray to prevent sticking.
- Sauté Aromatics and Make Roux: In a Dutch oven or heavy-bottomed large pot, melt the butter over medium heat. Add the finely chopped onion and cook for about 2 minutes until fragrant and slightly softened but not browned. Stir in the minced garlic and then sprinkle the white whole wheat flour on top. Whisk continuously until the flour is golden brown and lumps disappear, about 1 minute.
- Add Milk and Thicken Sauce: Gradually pour in the nonfat milk in small splashes while whisking constantly to avoid lumps. Bring the mixture to a simmer and cook, stirring often, until the sauce thickens and coats the back of the spoon, approximately 5 to 7 minutes.
- Season and Add Cheese: Remove the pot from heat. Stir in salt, ground black pepper, and cayenne pepper. Let the sauce cool for 1 minute, then fold in the Greek yogurt and shredded melty cheese until smooth and creamy. Add the cooked and drained pasta along with half of the sliced fresh basil. Gently stir to combine, coating each piece of pasta evenly with the cheese sauce. Taste and adjust seasoning if needed.
- Assemble and Bake: Transfer the pasta and cheese mixture to the prepared casserole dish. Evenly sprinkle the shredded parmesan over the top. Arrange the thin tomato slices over the cheese in a slightly overlapping pattern. Bake on the center rack for 15 to 20 minutes until the casserole is hot and bubbly throughout.
- Optional Broil for Crispiness: For a crispy golden top, switch the oven to broil and move the dish to the upper rack. Broil for 2 to 3 minutes, watching carefully to avoid burning, until the top is as dark and crispy as desired.
- Rest and Serve: Allow the baked macaroni and cheese to rest for 5 minutes to set. Sprinkle the remaining fresh basil over the top and serve immediately while hot and flavorful.
- Storage and Reheating: Store any leftovers in an airtight container in the refrigerator for up to 4 days. Reheat individual servings gently in the microwave with a splash of milk, stirring occasionally to maintain creaminess and prevent drying out.
Notes
- Use whole wheat pasta for added fiber and a nutty flavor.
- Choosing a melty cheese like sharp cheddar, fontina, or mozzarella ensures a smooth, creamy sauce.
- Greek yogurt adds creaminess and tang while reducing fat content.
- Adjust cayenne pepper to taste for desired spice level.
- Broiling the top is optional but provides a delicious crispy finish.
- Cool the cheese sauce slightly before adding yogurt to avoid curdling.
- Leftovers reheat best with a splash of milk to keep the texture creamy.
- Prep Time: 15 minutes
- Cook Time: 35 minutes
- Category: Main Dish
- Method: Baking
- Cuisine: American
Keywords: macaroni and cheese, tomato basil macaroni, whole wheat pasta, baked mac and cheese, healthy comfort food, Greek yogurt cheese sauce

