Cook the farro: Bring a pot of well-salted water to a boil. Add the farro and cook for 30–35 minutes, or until tender. Drain and set aside.
Preheat the oven: Preheat to 425°F (220°C).
Roast the vegetables: In a 9x13-inch roasting pan, combine red onions, red bell peppers, zucchini, olive oil, salt, and black pepper. Toss to coat evenly. Roast for 30–35 minutes, until the vegetables begin to caramelize and take on some color.
Reduce the oven temperature: Turn the oven down to 400°F (200°C).
Assemble the bake: Add the cooked farro, sun-dried tomatoes, pepperoni, smoked paprika, oregano, garlic, vegetable stock, and additional salt and pepper to taste directly into the roasting pan. Stir well to combine all ingredients.
Add the cheeses: Dollop spoonfuls of ricotta evenly over the top, then sprinkle the grated fontina cheese over the surface.
Bake: Return the dish to the oven and bake for 30 minutes, until the cheese is melted, bubbling, and golden in spots.
Serve: Remove from the oven and let cool slightly. Serve warm and enjoy!