Dice the onions, carrots, and celery into equal sized pieces. Cook on a medium-high heat until translucent with garlic, about 10 minutes.
Add the tomatoes, rosemary, thyme, chili flakes, and bay leaves. Bring to a boil then lower heat and bring to a simmer.
Heat 2 tbsp. of olive oil in a medium saucepan. Add the spinach, garlic, salt and pepper. Cook until spinach is wilted and still bright green, about 4-5 minutes. Set aside in a bowl and let cool. Once cooled, finely chop the spinach.
In a large bowl, combine the ricotta, lemon zest, spinach, eggs, and bread crumbs. Season with salt and pepper to taste.
Bring the tomatoe sauce to medium heat. Form the ricotta mixture into ping pong sized balls: these are now gnudi. Gently drop them into the sauce, cover and let cook for 10 to 12 minutes until they are firm.
Serve the gnudi into bowls and cover with sauce. Grate some parmesan cheese on top, serve and enjoy.
If you leave out the spinach and have plain ricotta Gnudi it will look like this.