Bring a large pot of salted water to a boil. Add the elbow macaroni and cook according to package directions until al dente. Drain the pasta and set it aside.
In a medium saucepan over medium heat, melt the butter. Once melted, whisk in the flour and cook for about 1 minute to form a smooth roux.
Gradually whisk in the milk, making sure there are no lumps. Keep stirring until the mixture begins to thicken—this should take about 5 minutes.
Reduce the heat to low, then add the shredded cheddar and pepper jack cheeses. Stir until the cheese is completely melted and the sauce is smooth.
Sprinkle in garlic powder, onion powder, cumin, smoked paprika, salt, and black pepper. Mix well to combine and let the flavors come together.
Add the cooked pasta to the cheese sauce, stirring until all the noodles are evenly coated. If you’re using add-ins like cooked chorizo, jalapeños, corn, or cilantro, stir them in now.
Let the macaroni and cheese cook for an additional 2–3 minutes to warm everything through and blend the flavors.
Spoon the Mexican mac and cheese into bowls. Garnish with extra cilantro or a sprinkle of chili powder, and serve hot.