Bring a large pot of salted water to a boil and cook the macaroni until just al dente. Before draining, scoop out some pasta water and set it aside. This reserved water helps adjust sauce consistency later.
Melt butter in a large skillet over medium heat and add onions, garlic, and bell peppers. Cook until softened and fragrant, stirring occasionally so nothing burns. This step creates the base flavor.
Add ground beef to the skillet and break it apart while cooking. Continue until browned and fully cooked, then season with salt, pepper, paprika, and chili flakes. Proper seasoning here makes the entire dish taste richer.
Lower the heat and stir in cream cheese, mozzarella, and cheese slices. Mix gently until melted and smooth, ensuring the sauce doesn’t overheat and separate.
Add cooked pasta and a splash of reserved pasta water into the skillet. Stir until noodles are coated evenly, adding more water if needed to achieve a creamy, silky sauce.