Dice onion, celery, carrots, bell pepper and garlic.
Heat olive oil in a large soup/stock pot over medium heat. Add onion, celery, carrots, bell pepper and garlic. Season with salt and red pepper flakes. Cook for 3 minutes.
Meanwhile, slice zucchini, yellow squash and mushrooms. Add to pot and continue cooking over medium heat for about 5 minutes, until mushrooms are browned and onions are translucent.
Stir in diced tomatoes, olives, capers, kidney beans, vegetable stock base (optional), and water. Increase heat and bring to a slow boil.
Stir in farro and seasonings, except optional parsley and nutritional yeast. Reduce heat to medium-low and simmer until farro is fully cooked, about 25 to 30 minutes.
To serve, sprinkle individual bowls with fresh parsley, nutritional yeast and some freshly ground black pepper, if desired.