Cook the chorizo and onion in a dutch oven or large pan over medium-high heat breaking up the chorizo as it cooks, about 5 minutes. Using a slotted spoon move the chorizo and onion mixture to a bowl lined with a paper towel. Drain any grease from the pan and wipe clean.
Return the chorizo and onion to the clean pan and place on the stove over medium-high heat. Add the garlic and cook while stirring until garlic becomes fragrant, about 1 to 2 minutes.
Add the tomato puree, beef broth, jalapeno, red pepper flakes, ½ tsp salt, and ¼ tsp pepper. Bring to a boil then stir in the macaroni, cover the pan and reduce heat to medium-low. Cook until pasta is tender, around 10 minutes.
Take off the heat and stir in the cheeses, add salt and pepper to taste.
