Preheat the oven: Set to 400°F (200°C).
Line a baking sheet with parchment paper.
Prep the peppers: Slice the tops off the bell peppers and scoop out seeds and membranes. Rub the outsides with 1 tablespoon olive oil and a pinch of salt. Place cut-side up in a baking dish and set aside.
Cook the quinoa: In a saucepan, combine rinsed quinoa and vegetable broth.
Bring to a boil, reduce to a simmer, cover, and cook for 15 minutes, or until liquid is absorbed. Fluff with a fork and set aside.
Roast the vegetables: On the lined baking sheet, toss onion, zucchini, cherry tomatoes, mushrooms, and diced bell pepper with 1 tablespoon olive oil, garlic, smoked paprika, oregano, cumin, red pepper flakes (if using), salt, and black pepper. Spread into an even layer and roast for 18–20 minutes, stirring once, until tender and lightly caramelized.
Combine the filling: In a large bowl, mix cooked quinoa, roasted vegetables, and chopped parsley.
Taste and adjust seasoning with more salt, pepper, or spices as needed. Stir in cheese if using.
Stuff the peppers: Spoon the filling into each pepper, packing it down gently. Fill to the top.
Bake: Cover the baking dish loosely with foil and bake for 25 minutes.
Remove foil and bake another 10 minutes, until peppers are tender and the tops are slightly golden.
Finish and serve: Let rest for 5 minutes. Squeeze lemon over the top for brightness and add extra herbs if you like. Serve warm.