Spicy Mac and Cheese with Harissa & 3 Cheeses

If you love my classic baked mac and cheese, think of this harissa macaroni and cheese as its bolder, spicier cousin. The smoky, earthy harissa cuts through every creamy, cheesy bite and gives classic comfort food a completely different personality. If you enjoy twists like this, don’t miss my curry mac and cheese either. And for even more control over the heat and flavor, try it with my homemade harissa.

Ingredients & Substitutions

• Elbow Macaroni – The classic shape for mac and cheese, with plenty of nooks to hold onto sauce. Shells, cavatappi, or penne work well as substitutes if that’s what you have on hand.
• Cheddar Cheese – Adds sharp, tangy flavor and great melt. Sharp or extra-sharp cheddar gives the boldest taste, but mild cheddar works if you prefer a gentler flavor.
• Gruyère Cheese – Brings a nutty, slightly sweet depth and ultra-smooth melt. Swiss or fontina are good substitutes if Gruyère isn’t available.
• Mozzarella Cheese – This is your stretch factor, giving the sauce that gooey, pull-apart quality. Low-moisture, part-skim mozzarella melts best; fresh mozzarella can make the sauce watery.
• Unsalted Butter – Forms the base of your roux, which thickens the cheese sauce. Using unsalted lets you control the saltiness, especially since cheese and harissa both add sodium.
• All-Purpose Flour – Combines with butter to make the roux that thickens your milk into a creamy sauce base. Gluten-free flour blends can work as a 1:1 swap if needed.
• Whole Milk – Creates a rich, creamy sauce. 2% milk works in a pinch, but the sauce will be slightly less rich; avoid skim milk, as the sauce may turn out thin.
• Harissa Paste – The star of the heat and smokiness here. Store-bought is convenient, but homemade lets you control the spice level. Start with less if you’re heat-sensitive. You can always add more, but you can’t take it away.
• Paprika – Adds warm color and mild smoky flavor that complements the harissa. Smoked paprika will intensify that smokiness even further.
• Garlic Powder & Onion Powder – Build savory depth without the texture of fresh aromatics. Fresh minced garlic and onion can be substituted, sautéed briefly in the butter before making the roux.

This is just a short review of the ingredients; for the complete recipe, including quantities, scroll down to the recipe card 👇

Video Recipe

Watch the video below to see exactly how I make this creamy spicy macaroni and cheese with harissa, from the roux and cheese sauce to the golden baked finish.

Prefer the written recipe? Scroll down to the recipe box 👇

What is Harissa?

Harissa is a North African chili paste most closely associated with Tunisian cuisine. It’s typically made with red chilies, garlic, olive oil, and warm spices such as cumin, coriander, and caraway, creating a smoky, earthy heat that’s much more complex than a simple hot sauce.

It’s commonly used in soups, stews, marinades, dips, and dishes like my harissa hummus. Here, it melts directly into the cheese sauce, adding smoky heat that balances beautifully with the rich cheddar and Gruyère.

Harissa can vary quite a bit in flavor and heat depending on the brand, so taste yours before adding more. You can use store-bought harissa or make my homemade harissa for even more control over the flavor and spice level.

How to Make Spicy Mac and Cheese with Harissa

Step 1: Cook the pasta. Preheat the oven to 350°F (180°C) and grease a 9×13-inch baking dish. Cook the macaroni 1–2 minutes less than the package directions, until just al dente, then drain.

Step 2: Make the harissa sauce. Melt the butter over medium-low heat, whisk in the flour, and cook for about 2 minutes without browning. Stir in the harissa for 30–60 seconds, then gradually whisk in the milk. Add the paprika, garlic powder, onion powder, salt, and pepper, and cook briefly until the sauce begins to thicken.

Step 3: Add the cheese and season. Combine the grated cheeses and reserve about one-quarter for topping. Reduce the heat to low and gradually stir the rest of the cheese into the sauce until melted and smooth. Keep the heat low and don’t let the sauce boil once the cheese is added. Taste and adjust the seasoning or harissa if needed.

Step 4: Combine. Add the cooked macaroni to the sauce and stir until completely coated. Don’t worry if the sauce looks a little loose at this point; it will thicken as it bakes and rests.

Step 5: Bake. Transfer to the baking dish, top with the reserved cheese, and bake for 20–25 minutes, until bubbling and lightly golden. Broil for 1–2 minutes for extra color, if desired, then rest for 5 minutes before serving.

Control The Heat 🌶️

One important thing to know about harissa is that the heat level varies significantly from brand to brand. Some are mild, smoky, and aromatic, while others can be surprisingly hot, so taste yours before deciding how much to use.

For a milder spicy mac and cheese, start with about half the harissa and add more to taste. You can add a little extra paprika for color and warmth without much additional heat. If you love things extra spicy, add another spoonful of harissa or a pinch of cayenne pepper to the sauce.

Why Does the Cheese Sauce Look So Thin?

Don’t worry if your cheese sauce looks thinner than expected before baking—that’s intentional. This recipe uses enough milk to keep the mac and cheese creamy after it goes into the oven. As it bakes, the sauce continues to thicken while the pasta absorbs some of the moisture. The sauce thickens even more as the mac and cheese rests after baking, giving you a creamy result rather than a dry, stiff one.

Choose Your Cheese (And Grate It Yourself)

I use a combination of cheddar, Gruyère, and mozzarella for the best balance of sharp flavor, creaminess, and stretch. But you can easily switch things up with other good melting cheeses like Gouda, Monterey Jack, fontina, Emmental, or provolone.

Whatever you choose, I highly recommend grating the cheese yourself. Pre-shredded cheese is often coated with anti-caking agents, which can prevent it from melting as smoothly and may leave your cheese sauce slightly grainy. Freshly grated cheese melts much better and gives you that silky, creamy sauce you want in mac and cheese.

Optional Variations & Dietary Adaptations

• Protein Boost – Stir in shredded rotisserie chicken, crispy bacon, or browned ground sausage when you combine the pasta and sauce for a heartier dish.
• Veggie Add-Ins – Roasted red peppers, sautéed spinach, or caramelized onions all pair beautifully with the smoky harissa flavor. Fold them in right before baking.
• Gluten-Free – Swap the elbow macaroni for your favorite gluten-free pasta and use a 1:1 gluten-free flour blend in place of all-purpose flour for the roux.
• Breadcrumb Topping – For extra crunch, mix ¾ cup (45 g) panko breadcrumbs with 2 tablespoons (30 g) melted butter. Sprinkle evenly over the mac and cheese before baking. You can also mix in 2–3 tablespoons of finely grated Parmesan for extra flavor.
• Stovetop Version – Skip the baking step and follow the method from my stovetop mac and cheese recipe, adding the harissa to the thickened sauce before adding the cheese. 

What to Serve with Spicy Mac and Cheese

This creamy, smoky harissa mac and cheese can absolutely be a meal on its own, but it also makes a fantastic side dish. Here are some of my favorite ways to build a complete meal around it.

Fresh Salads

Something crisp and refreshing is perfect for balancing all that rich cheese. Try my Green Goddess Salad, Celery Cucumber Salad, Creamy Cucumber Salad, or Healthy Chickpea Salad.

Add Some Protein

Turn your spicy mac and cheese into a heartier dinner with Baked Chicken Skewers, my Best Chicken Breast, or Chicken Schnitzel. All three are flavorful without competing too much with the smoky harissa flavor.

For the Ultimate Comfort-Food Meal

If you’re going all-in on comfort food, serve it alongside Crispy Fried Chicken, Homemade Chicken Nuggets, or warm Garlic Parmesan Dinner Rolls. Not exactly a light dinner, but definitely a delicious one.

How to Store Harissa Mac and Cheese

• Refrigerator: Store cooled leftover mac and cheese in an airtight container for up to 4 days.
• Freezer: Freeze individual portions in airtight freezer-safe containers for up to 2 months. Thaw overnight in the refrigerator before reheating. The sauce may change slightly in texture after freezing, but adding a little milk while reheating helps restore its creaminess.
• Reheating: For the best texture, warm leftovers gently on the stovetop over low heat with a splash of milk. You can also cover and bake at 350°F (175°C) for 15–20 minutes, or microwave individual portions in 30-second intervals. Avoid high heat, which can cause the cheese sauce to separate or become grainy.

More Mac and Cheese Recipes

• Creamy Baked Mac and Cheese Recipe
• Curry Macaroni and Cheese
• Easy 3-Ingredient Stovetop Mac and Cheese

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