Preheat and prep. Heat your oven to 375°F (190°C).
Lightly grease a standard 24-cup mini muffin tin with nonstick spray. You can also use a regular muffin tin for larger bites; just increase bake time slightly.
Cook the pasta. Boil the macaroni in well-salted water until just shy of al dente. It will keep cooking in the oven.
Drain and set aside.
Make the cheese sauce base. In a medium saucepan, melt 3 tablespoons butter over medium heat. Whisk in 3 tablespoons flour and cook 1–2 minutes until it smells toasty. Slowly whisk in 1 1/2 cups milk until smooth.
Simmer, whisking, until thickened and silky.
Add the flavor. Off the heat, stir in 1 1/2 cups sharp cheddar and 1/2 cup Gruyère or Jack until melted. Add 2 tablespoons cream cheese if using. Season with 1/2 teaspoon each garlic powder and onion powder, 1/2 teaspoon Dijon, a pinch of smoked paprika, and salt and pepper to taste.
Combine and bind. Stir the cooked pasta into the sauce.
Let the mixture cool for 5 minutes, then mix in 2 lightly beaten eggs. This step helps the bites hold together. The mixture should be thick and scoopable.
Portion into the pan. Spoon the mac mixture into each mini muffin cup, pressing lightly to compact.
Fill to the top for generous bites.
Top for crunch. Mix 1/2 cup panko with 1/4 cup grated Parmesan and a drizzle of olive oil or melted butter. Sprinkle over each cup for a crisp, savory crust.
Bake. Bake for 12–15 minutes (18–22 for standard muffin size), until the edges are bubbling and the tops are golden.
Cool and release. Let the bites cool in the pan for 5–10 minutes. Run a thin knife around the edges, then gently lift them out.
Cooling helps them set.
Serve. Enjoy warm with a simple dip like marinara, ranch, or a spicy ketchup. They’re also great plain—extra cheesy and satisfying.