Preheat the oven to 350°F (175°C) and spray a 9x13-inch baking dish with cooking spray.
Heat the olive oil in a large skillet over medium heat. Add the diced onion and cook until softened, about 4–5 minutes.
Add the minced garlic, chopped portobello, and diced red pepper to the skillet; sauté until the vegetables are tender, about 4–6 minutes. Remove from heat and let cool slightly.
In a large bowl, combine the ricotta, 1/4 cup of the shredded mozzarella, 1/4 cup of the grated Parmesan, and the egg. Stir until smooth.
Add the drained, chopped spinach, dried basil, crushed red pepper, and salt and freshly cracked pepper to taste; mix until well combined.
Fold the sautéed mushroom, onion, and red pepper mixture into the cheese and spinach filling.
Spread about 1/2 cup of marinara sauce over the bottom of the prepared baking dish.
Arrange the cooked jumbo shells in the dish and evenly spoon the ricotta-vegetable filling into each shell.
Pour the remaining marinara sauce over the stuffed shells, then sprinkle the remaining mozzarella and Parmesan over the top.
Cover the dish with foil and bake for 30 minutes. Remove the foil and bake an additional 5 minutes until cheese is melted and bubbly.
Let the shells rest a few minutes before serving warm.