Preheat the oven to 375°F (190°C).
Place the bell peppers upright in a baking dish and lightly brush the outside with olive oil.
In a medium skillet, heat the olive oil over medium heat. Add the chopped onion and cook for 3-4 minutes until softened.
Add the minced garlic to the skillet and cook for an additional 1 minute until fragrant.
Remove the skillet from heat and transfer the onion and garlic mixture to a mixing bowl.
Add the ricotta cheese, cooked quinoa, grated Parmesan, chopped spinach, diced tomato, dried oregano, salt, black pepper, and crushed red pepper flakes to the bowl. Mix well to combine all ingredients.
Spoon the ricotta mixture evenly into each bell pepper, filling them completely.
Sprinkle the shredded mozzarella cheese evenly over the tops of the stuffed peppers.
Cover the baking dish with aluminum foil and bake for 30 minutes.
Remove the foil and bake for an additional 10 minutes, or until the peppers are tender and the cheese is golden and bubbly.
Remove from the oven and let cool for 5 minutes before serving.