Cheesy Baked Penne Pasta

Introduction

Cheesy Baked Penne Pasta is the ultimate comfort food—a rich, creamy, and indulgent dish that brings warmth to your table with every bite. Whether you’re preparing a family dinner, hosting guests, or simply craving something hearty and satisfying, this baked pasta recipe delivers on flavor, texture, and nostalgia. With its golden-brown crust, tender penne noodles, and layers of melty cheese, it’s no wonder this dish has become a staple in homes around the world. It’s easy to make, endlessly customizable, and perfect for meal prep or potlucks. In this comprehensive guide, we’ll walk you through everything you need to know about Cheesy Baked Penne Pasta—from its history and ingredients to step-by-step instructions, expert tips, variations, health considerations, and more.

The History

Pasta bakes have roots stretching back centuries, evolving from simple peasant dishes in Italy where leftover pasta was combined with available cheeses and baked to create a warm, filling meal. The concept of baked pasta likely began in Southern Italy, where families used wood-fired ovens to reheat or repurpose meals. Over time, as access to dairy improved and culinary techniques evolved, richer versions emerged—featuring cream, béchamel, and multiple cheeses.

In the United States, baked pasta gained popularity during the 20th century, especially after World War II, when convenience foods like canned soups and processed cheese became common. Dishes such as “tuna noodle casserole” and “macaroni and cheese” paved the way for modern interpretations of baked pasta. Cheesy Baked Penne Pasta, while not traditional Italian per se, reflects a delicious fusion of Italian-American culinary innovation. Penne, with its tube-like shape and ridges, holds sauces exceptionally well, making it ideal for baking. Today, this dish symbolizes home cooking at its finest—comforting, crowd-pleasing, and deeply satisfying.

Ingredients Breakdown

The magic of Cheesy Baked Penne Pasta lies in its balance of textures and flavors, achieved through a carefully selected combination of ingredients. Here’s a detailed look at each component:

Penne Pasta: This short, cylindrical pasta with angled ends is perfect for holding onto thick sauces and cheese. Its hollow center allows sauce to seep inside, ensuring every bite is flavorful. You can use regular or whole wheat penne depending on your preference.
Olive Oil: Used to prevent sticking when boiling pasta and adds a subtle fruity richness to the base.
Garlic: Fresh garlic provides an aromatic foundation. Sautéed gently in butter or oil, it infuses the entire dish with savory depth.
Butter: Adds creaminess and enhances mouthfeel, especially when used to make a roux for the sauce.
All-Purpose Flour: Acts as a thickening agent when creating a béchamel or cheese sauce, helping bind the ingredients together without becoming runny after baking.
Milk (whole preferred): Forms the liquid base of the sauce. Whole milk contributes to a richer, silkier texture compared to low-fat alternatives.
Heavy Cream (optional): For extra decadence, heavy cream can be added to the sauce, giving it a luxurious, velvety consistency.
Shredded Mozzarella Cheese: Melts beautifully and creates that iconic stretchy pull. Part-skim or full-fat both work, though full-fat yields better browning and flavor.
Grated Parmesan Cheese: Offers a salty, nutty punch and helps form a golden crust on top. Freshly grated is always superior to pre-grated, which often contains anti-caking agents.
Ricotta Cheese (optional): Sometimes layered into the dish for pockets of creamy texture. Can also be mixed into the sauce for added body.
Seasonings: Salt, black pepper, nutmeg (a pinch enhances dairy flavors), dried oregano, basil, and red pepper flakes add complexity and warmth.
Tomato Sauce (optional): While some versions are white (alfredo-style), others incorporate marinara or crushed tomatoes for a tomato-cheese hybrid bake.
Fresh Herbs (parsley, basil): Added at the end for brightness and color contrast.
Breadcrumbs (optional topping): Mixed with melted butter and Parmesan, they create a crispy, golden topping that contrasts wonderfully with the soft interior.

Step-by-Step Recipe

Preheat Oven: Begin by preheating your oven to 375°F (190°C). This ensures even baking and proper cheese melting.
Cook the Pasta: Bring a large pot of salted water to a boil. Add 1 pound (450g) of penne and cook until al dente—usually 1–2 minutes less than package instructions. Drain and toss with a little olive oil to prevent sticking. Set aside.
Prepare the Cheese Sauce: In a medium saucepan, melt 3 tablespoons of butter over medium heat. Add 2 minced garlic cloves and sauté for 30 seconds until fragrant. Stir in 3 tablespoons of all-purpose flour to form a roux. Cook for 1–2 minutes, stirring constantly, to remove raw flour taste.
Add Liquids: Gradually whisk in 2 cups of whole milk and ½ cup of heavy cream (if using). Continue whisking until the mixture thickens and comes to a gentle simmer—about 5–7 minutes. Reduce heat if needed to prevent scorching.
Incorporate Cheese: Remove the sauce from heat. Stir in 2 cups shredded mozzarella, ¾ cup grated Parmesan, ½ cup ricotta (if using), ½ teaspoon salt, ¼ teaspoon black pepper, ¼ teaspoon nutmeg, ½ teaspoon dried oregano, and a pinch of red pepper flakes. Mix until smooth and fully combined.
Combine Pasta and Sauce: In a large mixing bowl, combine the cooked penne with the cheese sauce. Gently fold together until all noodles are evenly coated. Taste and adjust seasoning if necessary.
Transfer to Baking Dish: Pour the mixture into a greased 9×13 inch (23×33 cm) baking dish. Spread evenly with a spatula.
Add Topping (Optional): Sprinkle the top with additional mozzarella and Parmesan (½ cup total), plus a layer of buttered breadcrumbs (½ cup panko mixed with 1 tablespoon melted butter and 2 tablespoons Parmesan).
Bake: Place in the preheated oven and bake for 25–30 minutes, or until the top is golden brown and bubbling around the edges.
Rest and Serve: Let the baked penne rest for 5–10 minutes before serving. This allows the sauce to set slightly, making it easier to serve cleanly. Garnish with chopped fresh parsley or basil.

Tips

Don’t Overcook the Pasta: Since the penne will continue cooking in the oven, boiling it to al dente prevents mushiness. Test early and drain promptly.
Use Freshly Grated Cheese: Pre-shredded cheese contains cellulose to prevent clumping, which can interfere with melting and create a grainy sauce.
Temper the Milk: When adding milk to the roux, do so gradually while whisking continuously to avoid lumps.
Layer Creatively: For visual appeal and texture variation, consider layering: half the sauced pasta, a sprinkle of extra cheese or ricotta dollops, then the rest of the pasta.
Browning the Top: If the top isn’t browning enough after baking, switch the oven to broil for 1–2 minutes—but watch closely to avoid burning.
Let It Rest: Allowing the dish to sit after baking helps it hold its shape when scooped and improves overall texture.
Grease the Pan Well: Use non-stick spray, butter, or oil to ensure easy removal and cleanup.
Double the Batch: This dish reheats well and freezes beautifully—ideal for meal prepping or feeding a crowd.

Variations and Customizations

Cheesy Baked Penne Pasta is incredibly versatile. Here are some popular twists to personalize the dish:

Vegetable-Packed Version: Add sautéed spinach, roasted broccoli, caramelized onions, sun-dried tomatoes, or sautéed mushrooms for added nutrition and flavor.
Protein Boost: Mix in cooked Italian sausage, ground beef, grilled chicken, pepperoni, bacon, or plant-based crumbles for a heartier meal.
Seafood Twist: Fold in flaked salmon, shrimp, or crab meat for a gourmet take.
Spicy Kick: Increase red pepper flakes or add diced jalapeños, Calabrian chilies, or hot sauce to the sauce.
Four-Cheese Bake: Combine mozzarella, Parmesan, provolone, and gorgonzola for a bold, complex cheese profile.
White vs. Red Sauce: Use a creamy Alfredo-style base for a white version, or mix in 1–2 cups of marinara sauce for a classic baked ziti-style red version.
Dairy-Free Option: Substitute with plant-based butter, almond or oat milk, and vegan cheeses made from cashews or coconut.
Gluten-Free Adaptation: Use gluten-free penne and a GF flour blend for the roux. Ensure all other ingredients are certified gluten-free.
Keto-Friendly Version: Replace pasta with spiralized cauliflower or zucchini noodles, thicken sauce with xanthan gum instead of flour, and use high-fat dairy.
Breakfast Bake: Add scrambled eggs, diced ham, and cheddar cheese for a brunch-inspired cheesy penne casserole.

Health Considerations and Nutritional Value

While undeniably delicious, Cheesy Baked Penne Pasta is a rich dish that should be enjoyed in moderation, especially for those monitoring calories, fat, sodium, or carbohydrates. However, with thoughtful adjustments, it can fit into a balanced diet.

Nutritional Profile (Approximate per serving, 1/6 of recipe):

Calories: ~450–550
Total Fat: 20–28g (Saturated Fat: 10–14g)
Cholesterol: 60–80mg
Sodium: 600–900mg (varies based on cheese and added salt)
Carbohydrates: 45–55g (Fiber: 2–4g, Sugar: 4–6g)
Protein: 18–22g

Health Tips:

Reduce Fat: Use part-skim mozzarella, low-fat milk, and limit cream or butter. Replace half the cheese with nutritional yeast for a cheesy flavor with fewer calories.
Boost Fiber: Opt for whole wheat or legume-based penne, which increases fiber and protein content.
Lower Sodium: Choose low-sodium cheeses, reduce added salt, and enhance flavor with herbs and spices instead.
Add Veggies: Incorporating vegetables increases vitamins, minerals, and fiber while reducing the calorie density of the dish.
Portion Control: Serve with a side salad or steamed greens to balance the meal and promote satiety.
Heart-Healthy Swaps: Use olive oil instead of butter and include omega-3-rich additions like spinach or walnuts.

Ingredients

1 pound (450g) penne pasta
1 tablespoon olive oil
3 tablespoons unsalted butter
2 cloves garlic, minced
3 tablespoons all-purpose flour
2 cups whole milk
½ cup heavy cream (optional, for extra richness)
2 cups shredded mozzarella cheese, divided
¾ cup grated Parmesan cheese, divided
½ cup ricotta cheese (optional)
½ teaspoon salt (or to taste)
¼ teaspoon black pepper
¼ teaspoon ground nutmeg
½ teaspoon dried oregano
Pinch of red pepper flakes (optional)
½ cup panko breadcrumbs (optional, for topping)
1 tablespoon melted butter (for breadcrumb topping)
Fresh parsley or basil, chopped (for garnish)

Directions

Preheat oven to 375°F (190°C). Grease a 9×13 inch baking dish and set aside.
Bring a large pot of salted water to a boil. Add penne and cook until al dente (about 8–9 minutes). Drain, drizzle with olive oil, and set aside.
In a saucepan over medium heat, melt 3 tablespoons butter. Add garlic and sauté for 30 seconds.
Stir in flour and cook for 1–2 minutes, stirring constantly, to form a roux.
Gradually whisk in milk and cream. Continue cooking, whisking frequently, until the sauce thickens and coats the back of a spoon (5–7 minutes).
Remove from heat. Stir in 1½ cups mozzarella, ½ cup Parmesan, ricotta (if using), salt, pepper, nutmeg, oregano, and red pepper flakes. Mix until smooth.
Fold the cooked penne into the cheese sauce until well combined.
Pour into the prepared baking dish. Top with remaining ½ cup mozzarella, ¼ cup Parmesan, and optional breadcrumb mixture (panko + 1 tbsp melted butter + 2 tbsp Parmesan).
Bake for 25–30 minutes, until bubbly and golden on top.
Let stand for 5–10 minutes before serving. Garnish with fresh herbs and enjoy!

FAQ

Can I make Cheesy Baked Penne ahead of time?
Yes! Assemble the dish, cover, and refrigerate for up to 24 hours before baking. Add 5–10 minutes to the baking time if starting cold.

How do I reheat leftovers?
Reheat individual portions in the microwave with a splash of milk to restore creaminess. For larger amounts, cover with foil and bake at 350°F for 15–20 minutes.

Can I freeze this dish?
Absolutely. Freeze unbaked or baked penne in an airtight container for up to 3 months. Thaw overnight in the fridge before baking or reheating.

Why is my sauce lumpy?
Lumps usually come from adding milk too quickly or not whisking enough. Always temper the milk into the roux gradually while whisking.

What can I serve with Cheesy Baked Penne?
Pair with a crisp green salad, garlic bread, roasted vegetables, or a light soup like minestrone.

Can I use different pasta?
Yes—ziti, rigatoni, fusilli, or shells work well due to their ability to hold sauce.

Is this dish kid-friendly?
Definitely! Most children love the cheesy, mild flavor. You can hide pureed veggies in the sauce for picky eaters.

Summary

Cheesy Baked Penne Pasta is a rich, comforting dish that combines perfectly cooked penne with a creamy, multi-cheese sauce and a golden, bubbling top—baked to perfection and ideal for sharing. Easy to customize, freezer-friendly, and deeply satisfying, it’s a timeless favorite for weeknights, gatherings, or anytime you crave a warm, cheesy embrace on a plate.