Bring a large pot of heavily salted water to a boil and cook the macaroni according to the package directions. Drain, saving about ½ cup of the pasta cooking water.
Heat oil in a large skillet over medium-high heat. Add the onions and cook, stirring occasionally, until softened, about 5 minutes. Add the garlic and jalapeño and cook, stirring for 1 minute. Lower the heat to medium-low, add the queso and macaroni and stir well. If the sauce seems a little dry, add some of the pasta cooking water. Cook for about 3 minutes or until everything is hot and the sauce is thick.
Preheat the broiler to high. Pour the mixture into a greased 9x12-ich (or similar) baking dish, top with the crushed croutons and place until the broiler, about 6 inches from the heat source, for 1-2 minutes. Watch carefully so the croutons don’t burn.