Preheat your oven to 200°C (390°F). Slice the tops off the peppers and carefully remove the seeds and membranes, creating hollow vessels. Place them cut-side up in a baking dish lined with parchment paper.
Heat olive oil in a large skillet over medium heat until it shimmers. Add chopped onion and cook, stirring frequently, until it becomes translucent and fragrant, about 5 minutes. Add minced garlic and cook for another minute until aromatic.
Stir in cooked quinoa and black beans, then sprinkle in smoked paprika, cumin, and chili flakes if using. Cook for 3-4 minutes, stirring to combine and warm everything through. The mixture should look vibrant and slightly fragrant.
Remove the skillet from heat and stir in chopped cilantro, lemon juice, and toasted seeds for added texture and brightness. Taste and adjust seasoning if needed. Let the filling cool slightly for a few minutes.
Gently spoon the filling into each hollowed pepper, pressing down softly to pack it in evenly. Fill all peppers completely and place them in the prepared baking dish.
Cover the dish with aluminum foil and bake for 30 minutes, until peppers are tender and slightly blistered at the edges. Remove the foil and bake for an additional 10 minutes to develop a nice char and deepen the smoky flavor.
Check that the peppers are tender and the filling is hot and fragrant. The skins should be blistered and slightly blackened for that smoky effect. Remove from oven and let rest for 5 minutes.
Garnish with additional cilantro and a squeeze of lemon for a bright, fresh finish. Serve hot, perhaps with a drizzle of olive oil or a side salad.
