Gluten-Free Baked Mac and Cheese with Three Cheeses

Why You’ll Love This Recipe

• Ultra-creamy, silky three-cheese sauce that clings to every noodle.
• Crisp, buttery gluten-free breadcrumb topping with broiled golden edges.
• Simple, reliable method with only certified gluten-free ingredients.
• Family-friendly comfort food that bakes in under 20 minutes.

Grocery List

• Produce: Fresh flat-leaf parsley (optional garnish)
• Dairy: Unsalted butter, whole milk, sharp cheddar, Gruyère, Parmesan
• Pantry: Certified gluten-free elbow macaroni, gluten-free all-purpose flour (1:1 blend), gluten-free panko breadcrumbs, ground mustard, garlic powder, onion powder, paprika, black or white pepper, kosher or sea salt, olive oil or extra butter to grease the dish

Full Ingredients

Pasta

• 12 oz (340 g) certified gluten-free elbow macaroni (or GF cavatappi)
• 1 tbsp kosher salt (for boiling water)

Three-Cheese Sauce

• 4 tbsp (56 g) unsalted butter
• 1/4 cup (30 g) gluten-free all-purpose flour (1:1 blend with xanthan gum)
• 3 cups (720 ml) whole milk, warmed
• 8 oz (225 g) sharp cheddar, freshly grated
• 4 oz (115 g) Gruyère, freshly grated
• 2 oz (60 g) Parmesan, finely grated (reserve 2 tbsp/10 g for topping)
• 1 tsp ground mustard (dry mustard)
• 1/2 tsp garlic powder
• 1/2 tsp onion powder
• 1/2 tsp paprika (smoked or sweet)
• 1/4 tsp ground white or black pepper
• 3/4 tsp fine sea salt, or to taste

Crispy Gluten-Free Topping

• 1 cup (about 50 g) gluten-free panko breadcrumbs
• 2 tbsp (28 g) unsalted butter, melted
• Reserved 2 tbsp finely grated Parmesan (from above)
• 1 tbsp finely chopped fresh parsley (optional)

To Prep the Dish

• 1 tsp olive oil or butter, for greasing the baking dish

Step-by-Step Instructions

Step 1: Preheat and prep

Place a rack in the center of the oven and heat to 375°F (190°C). Lightly grease a 9×13-inch (3-quart) baking dish with olive oil or butter. Warm the milk in a small saucepan or microwave until just warm to the touch; this helps the sauce thicken smoothly. Grate all cheeses and reserve 2 tablespoons of the Parmesan for the topping.

Step 2: Boil the gluten-free pasta

Bring a large pot of water to a boil and season with 1 tablespoon kosher salt. Add the gluten-free elbow macaroni and cook until very al dente—about 1 to 2 minutes less than the package directs. Drain well. If not using immediately, toss with a teaspoon of olive oil to prevent sticking.

Step 3: Make a gluten-free roux

In a large saucepan or Dutch oven, melt 4 tablespoons butter over medium heat. Sprinkle in the gluten-free flour and whisk constantly for 2 minutes; the mixture will be foamy and fragrant, but should not brown. Slowly pour in the warmed milk while whisking, ensuring no lumps form. Continue cooking, whisking often, until the sauce gently bubbles and thickens enough to coat the back of a spoon, 3 to 5 minutes.

Step 4: Build the three-cheese sauce

Remove the pan from heat. Season with ground mustard, garlic powder, onion powder, paprika, pepper, and 3/4 teaspoon salt. Add the cheddar, Gruyère, and all but the reserved Parmesan in small handfuls, whisking after each addition until melted and smooth. Taste and adjust seasoning; remember the topping adds a salty-savory note.

Step 5: Combine pasta and sauce

Add the drained pasta to the cheese sauce and fold gently to coat every piece. If the sauce seems very thick, stir in 2 to 3 tablespoons hot water or milk to loosen slightly. Spread the mixture evenly into the prepared baking dish, smoothing the top.

Step 6: Mix the topping and bake

In a bowl, toss the gluten-free panko with the melted butter and the reserved Parmesan until evenly moistened. Stir in parsley if using. Sprinkle the topping over the mac and cheese in an even layer. Bake uncovered until the edges are bubbling and the topping is lightly golden, about 15 minutes. Switch the oven to broil and broil 2 to 3 minutes, watching closely, until the crumbs are deeply golden and the edges are bronzed.

Step 7: Rest and serve

Let the baked mac and cheese rest for 5 to 10 minutes to set. Garnish with a little extra parsley if you like. Serve warm with a crisp green salad.

Pro Tips

• Cook gluten-free pasta slightly under al dente; it softens further in the oven.
• Warm milk prevents a lumpy sauce and speeds thickening.
• Grate cheese from blocks for the smoothest melt; pre-shredded often contains anti-caking agents.
• Take the pan off heat before adding cheese to avoid a grainy sauce.
• Always check labels for certified gluten-free pasta, flour blends, and panko to avoid cross-contact.

Variations

• Smoky twist: Add 1/2 teaspoon smoked paprika to the sauce and scatter 4 strips of chopped, cooked gluten-free bacon over the pasta before topping.
• Herb and garlic: Stir 1 minced garlic clove (sautéed briefly in the butter before making the roux) and 1 tablespoon chopped chives into the sauce.
• Cheese swap: Replace Gruyère with fontina or use Pecorino Romano instead of Parmesan for a sharper bite.

Storage & Make-Ahead

Refrigerate leftovers in an airtight container for up to 4 days. Reheat, covered, at 325°F (165°C) for 15 to 20 minutes; uncover and broil 1 to 2 minutes to re-crisp the topping. Microwave reheating also works—use 60 to 70 percent power and short intervals, then finish under the broiler for crunch. Make-ahead: Assemble through Step 5, cool, cover, and refrigerate up to 24 hours. Mix the topping just before baking. Bake 20 to 25 minutes from cold, then broil to brown. Freezing note: Gluten-free pasta can soften when frozen; for best results, freeze the sauce alone up to 2 months and boil fresh GF pasta when ready to bake.

Nutrition (per serving)

Approximate: 700 calories; 36 g fat; 58 g carbs; 30 g protein; 2 g fiber; 910 mg sodium.