In a large pot or Dutch oven, heat the olive oil over medium high heat. Add the onion, mushrooms, and peppers and sauté for 4 minutes, until translucent. Add 1/2 teaspoon kosher salt, the garlic, oregano, fennel, and red pepper flakes and cook 2 to 3 minutes until fragrant and the veggies have softened.
Add the pizza sauce, canned tomatoes and their liquid, and vegetable broth. Bring to a boil, then reduce heat and simmer 10 minutes. Stir in the cheese and simmer 5 more minutes until it is melted. Taste and add additional kosher salt if necessary.
Serve warm topped with homemade croutons, additional Parmesan cheese, and fresh basil leaves (or simply serve with crusty bread or a gluten free bread substitute).