Preheat your oven to 190°C (375°F). Place a rack in the middle for even baking.
Slice off the tops of the bell peppers and carefully scoop out the seeds and membranes, creating a hollow cavity for the filling. Arrange the peppers upright in a baking dish.
Heat olive oil in a large skillet over medium heat. Add chopped onion and sauté until translucent and fragrant, about 5 minutes, until it begins to soften and turn slightly golden.
Add the minced garlic, cumin, and smoked paprika to the skillet. Cook for another 30 seconds until the mixture is fragrant and the garlic is just beginning to brown.
Stir in the cooked quinoa and black beans, mixing well to combine all ingredients evenly. Cook for 2-3 minutes until heated through.
Remove the skillet from heat and chop the cilantro. Stir most of it into the mixture, saving some for garnish. Squeeze fresh lime juice over the filling and season with salt and pepper to taste. Mix well.
Use a spoon or scoop to fill each hollowed-out pepper with the quinoa and bean mixture, pressing down gently to pack the filling without spilling over.
Sprinkle shredded cheese evenly over the top of each stuffed pepper. Cover the baking dish with aluminum foil if you want to prevent over-browning.
Bake in the preheated oven for 25-30 minutes until the peppers are tender when pierced with a fork and the cheese is melted, bubbly, and golden brown on top.
Remove from oven and let sit for 5 minutes to settle. Garnish with the remaining chopped cilantro and a squeeze of fresh lime for a bright finish.
Serve hot, enjoying the smoky, herbaceous flavors and tender, colorful peppers with melted cheese on top.
