Bring a large pot of heavily salted water to a boil; add the pasta and cook according to the directions on the package.

While the pasta cooks, add the bacon to a cold pan. Turn the heat to medium and cook until the fat renders and the bacon crisps, about 7 minutes. Add the butter, onion, bell pepper, garlic, and jalapeno; cook until softened, about 10 minutes. Sprinkle with flour and cook 1 minute.

Pour in the broth and milk and cook until the mixture begins to thicken and starts to bubble, about 10 minutes. Slowly stir in the cheese and sour cream. Drain the pasta, then stir into the sauce.