Grate the cheeses and measure your milk and pasta. Freshly shred the cheddar and Gruyère and keep them refrigerated until ready — freshly shredded cheese melts more smoothly because pre-shredded cheese typically contains anti-caking agents that can make the sauce grainy. Measure the milk and set aside.

Bring a large pot of salted water to a boil and cook the macaroni for 6 minutes — stop well before al dente (about 2–3 minutes shy of package instructions). Cooking the pasta slightly underdone matters because it will continue to soften in the slow cooker; starting al dente prevents a mushy final texture.

While the pasta cooks, make a quick roux on the stovetop: melt 2 tablespoons butter in a medium saucepan over medium heat. Add the 2 tablespoons flour and whisk continuously for 90 seconds until the flour loses its raw smell and the roux turns a pale blond. Cooking the flour removes the raw edge and gives the sauce body so it won’t be thin after hours in the crockpot.

Slowly whisk 1 cup of the milk into the roux to create a smooth paste, then whisk in the remaining 3 cups in a steady stream. Bring the mixture to a gentle simmer (small bubbles at the edge) for 2–3 minutes until it thickens slightly — this builds a béchamel-like base that helps the cheese suspend evenly and avoids an oily sauce.

Turn off the heat and whisk in the mustard powder, smoked paprika, salt, and pepper. These seasonings brighten the dairy and add a subtle background note that keeps the cheese from tasting flat.

Transfer the undercooked macaroni to a 4–6 quart slow cooker and pour the warm milk-roux mixture over it. Stir gently to combine so every piece of pasta is coated — even distribution prevents dry pockets and ensures even cooking.

Add about two-thirds of the shredded cheese to the slow cooker and fold it in gently. Reserve the remaining cheese for the final melt. Adding a portion now and finishing with the rest prevents overcooking the cheese and helps maintain a silky texture; prolonged exposure to low heat can make cheese seize and become grainy if added all at once.

Cover and cook on LOW for 1.5 to 2 hours. Check at 60 minutes and stir gently to redistribute heat and prevent sticking to the sides. Slow, gentle heat lets the proteins and fat in the cheese emulsify into the béchamel slowly, producing a glossy, clingy sauce rather than a separated one.

When the pasta is tender and the sauce is creamy (timing depends on your slow cooker model), stir in the remaining cheese and 1 tablespoon butter (if using). The residual heat will melt the final cheese quickly; stirring at the end prevents overcooking while creating a smooth, velvety finish.

Taste and adjust seasoning with salt and pepper. If the sauce is too thin, transfer to a saucepan and simmer gently for 3–5 minutes to reduce; if it’s too thick, whisk in 2–4 tablespoons milk until you reach the desired consistency. Serve immediately — mac and cheese is best the day it’s made for glossy sauce and ideal texture.