Preheat your oven to 180°C (356°F). Carefully cut the tops off the bell peppers and remove seeds and membranes. Arrange them upright in a baking dish.
In a pan, heat olive oil over medium heat and add the chopped onion. Sauté for about 3 minutes until it becomes fragrant and slightly translucent.
Add the minced garlic to the pan and cook for another minute, until it smells fragrant and begins to soften.
Mix in the cooked quinoa, drained tomatoes, cooked beans, paprika, salt, and pepper. Stir everything well and cook for 8-10 minutes until the mixture is heated through and slightly thickened.
Use a spoon to fill each pepper generously with the hearty mixture, pressing down lightly to pack it in.
Sprinkle the nutritional yeast evenly over the filled peppers for a cheesy accent.
Place the baking dish in the oven and bake for 25-30 minutes, until the peppers are soft and slightly blistered, and the filling is bubbling.
Remove from the oven and let the peppers rest for 5 minutes, allowing the flavors to meld and the filling to set slightly.
Garnish with fresh herbs if desired, then serve hot, enjoying the tender peppers and flavorful filling.