Macaroni and Cheese Recipe With Penne Pasta: Baked Three-Cheese Indulgence

There’s a reason baked penne mac and cheese remains a timeless comfort dish—it delivers restaurant-quality results with minimal effort.

This version uses three cheeses for depth and a crispy topping that contrasts beautifully with the creamy interior. I developed it in my small Boston kitchen after many trials to perfect the texture.

The penne holds sauce better than traditional macaroni, ensuring every bite is packed with flavor. Baking at high heat creates a golden crust while keeping the center velvety smooth.

Ideal for family dinners or potlucks, this dish proves that indulgence can be both simple and satisfying.

Ingredients for Macaroni and Cheese Recipe with Penne Pasta

Penne, three melty cheeses, and a crispy topping bring this comfort classic to life.

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The cheese selection elevates this dish. Cabot sharp cheddar has the right melt and tang, while Gruyère from Whole Foods adds that nutty depth you can’t skip. For Parmesan, Parmigiano-Reggiano wedge is non-negotiable—pre-grated lacks the texture and flavor. The penne should be al dente (check the package for cook time), as it bakes further in the oven. I always grab mine from De Cecco for consistent quality.

Short on time? Pre-shredded cheese blend works in a pinch, but it won’t melt as smoothly. No Gruyère? Fontina or Monterey Jack at equal amounts. For a gluten-free version, swap the flour for cornstarch (use half the amount). The Dijon adds depth, but yellow mustard gets you 80% there. Fresh nutmeg is worth the effort—ground from a whole nut tastes brighter than the jarred stuff.

Assemble and refrigerate unbaked for up to 24 hours. Leftovers keep 4-5 days in the fridge, though the topping softens. Reheat covered at 350°F for 15-20 minutes. This freezes beautifully for 3 months—just thaw overnight before reheating.

Step-by-Step Instructions for Baked Three-Cheese Penne

Here’s the method that guarantees creamy, cheesy perfection with a crisp topping.

Step 1: Cook Penne to Al Dente

Bring a large pot of salted water to a rolling boil. Add the 12 oz penne pasta and cook according to package directions for al dente, about 1 minute less than the suggested time. This ensures the pasta absorbs the sauce beautifully without turning mushy.

Drain the pasta in a colander and immediately return it to the pot. Toss with 1 teaspoon salt and ½ teaspoon black pepper while it’s hot. The residual heat helps the seasoning stick, and slightly undercooked pasta prevents it from overcooking during baking.

Step 2: Create a Rich, Creamy Béchamel Base

In a large saucepan over medium heat, melt the ½ cup unsalted butter. Once foaming subsides, whisk in the ⅓ cup all-purpose flour to form a smooth roux. Cook for 2-3 minutes until the mixture turns a pale golden color—this removes the raw flour taste.

Gradually pour in the 3 cups whole milk, whisking constantly to prevent lumps. Bring to a gentle simmer and cook for 3-4 minutes until the sauce thickens enough to coat the back of a spoon. Stir in the 1 tablespoon Dijon mustard, 2 minced garlic cloves, and ¼ teaspoon ground nutmeg for depth of flavor.

Step 3: Build the Cheese Sauce

Reduce heat to low and add the 2 cups sharp cheddar cheese and 1 cup Gruyère cheese in small handfuls, stirring continuously until each addition melts completely. This gradual addition prevents the sauce from breaking or becoming grainy.

Taste and adjust seasoning if needed. The sauce should be velvety smooth with a rich, tangy depth from the mustard and nutmeg. Fold in the cooked penne pasta until every piece is evenly coated. The sauce will thicken slightly as it absorbs into the pasta.

Step 4: Assemble and Top for Baking

Transfer the cheesy pasta to a greased 9×13-inch baking dish. Sprinkle the ½ cup Parmesan cheese evenly over the top, then distribute the ¾ cup panko breadcrumbs in an even layer. The Parmesan adds a salty depth while the panko creates a crispy, golden crust.

Press down lightly on the breadcrumbs to help them adhere to the sauce below. This prevents them from blowing around in the oven and ensures an even, crunchy topping. The dish is now ready for the oven.

Step 5: Bake to Golden Perfection

Bake at 375°F for 20-25 minutes until the top is golden brown and the edges are bubbling. The breadcrumbs should look toasted, and the sauce beneath should be thick and gooey.

Let it rest for 5 minutes before serving to allow the sauce to set slightly. Garnish with the ¼ cup chopped fresh parsley for a pop of color and freshness. The contrast of the crispy topping and creamy pasta underneath is what makes this dish unforgettable.

Wine and Beer Pairings for This macaroni and cheese recipe with penne pasta

White Wine Pairings

A crisp Chardonnay with bright acidity cuts through the richness of this dish. I prefer unoaked versions from California—like Kendall-Jackson Avant—to avoid overwhelming the cheese flavors. The citrus notes cleanse your palate beautifully. 🍷

Red Wine Options

A light Pinot Noir from Oregon works surprisingly well, especially with the nutty Gruyère. Try Meiomi Pinot Noir for its balanced fruit and earth notes. The wine’s subtlety complements rather than competes with the dish.

Beer Pairings

For beer lovers, a Belgian-style witbier like Blue Moon offers citrus and spice that brighten each bite. The effervescence also helps cut through the creaminess. A New England IPA works too—try Hazy Little Thing from New Belgium. 🍺

Non-Alcoholic Choices

A dry sparkling apple cider from Downeast Cider House in Boston provides the same palate-cleansing effect as wine. The bubbles and slight tartness balance the richness perfectly.

Cocktail Match

For a spirit option, a Bourbon Old Fashioned with its caramel and vanilla notes pairs wonderfully with the cheesy depth. I use Buffalo Trace for a smooth, approachable choice.

Frequently Asked Questions