Heat the extra virgin olive oil in a large pot over medium heat.
Add the chopped onion, diced carrots, and diced celery to the pot. Cook, stirring occasionally, until the vegetables are softened, about 7 minutes.
Add the minced garlic, dried thyme, dried rosemary, and crushed red pepper flakes. Cook for 1 minute until fragrant.
Pour in the vegetable broth, then add the drained cannellini beans, diced tomatoes with their juice, and the bay leaf. Stir to combine.
Bring the soup to a boil, then reduce the heat to low and simmer uncovered for 30 minutes, stirring occasionally.
Remove the bay leaf. Using an immersion blender, partially puree the soup to thicken it while leaving some beans and vegetables whole for texture. Alternatively, transfer about half the soup to a blender, puree, and return to the pot.
Add salt and freshly ground black pepper to taste.
Stir in the chopped fresh spinach and cook for an additional 5 minutes until the spinach is wilted.
Remove the pot from heat and stir in the chopped fresh parsley.
Ladle the soup into bowls and top with grated Parmesan cheese if desired. Serve warm.