In a large pot with a lid, heat oil over medium heat. Add onions and cook until the edges begin to turn translucent, about 5 minutes.
Add ground beef and cook, breaking the meat into crumbles as you go, until meat is browned.
Stir in garlic and cook for 30 seconds before adding tomato paste, salt, oregano, basil, pepper, and optional red pepper flakes. Stir until the meat is well-coated and you can really begin to smell the garlic and spices, 1 to 2 minutes.
Add crushed tomatoes, chicken broth, soy sauce, and bay leaves and bring to a simmer. Cover and simmer, stirring occasionally, for 25 minutes.
Remove bay leaves, stir in the macaroni, and cover. Simmer covered, stirring occasionally, until pasta is al dente, about 10 to 15 minutes.
Turn off heat and add cheese. Replace lid and let sit for 2 to 3 minutes until cheese is melted. Serve and enjoy!