Cook the quinoa: Add the rinsed quinoa and vegetable broth to a medium saucepan. Bring to a boil, cover, and reduce the heat to low. Simmer for 15 minutes. Remove from the heat and let stand, covered, for 5 minutes. Fluff with a fork.
Sauté the vegetables: Preheat the oven to 375°F (190°C) and lightly grease a 9 × 13-inch baking dish. Heat the olive oil in a large skillet over medium heat. Cook the onion and bell pepper for 5–6 minutes, until softened. Add the garlic, cumin, smoked paprika, chili powder, oregano, salt, and black pepper and cook for 30 seconds.
Mix the filling: In a large bowl, combine the cooked quinoa, sautéed vegetables, black beans, corn, drained tomatoes, 1½ cups enchilada sauce, 1 cup cheese, cilantro, and lime juice. Stir gently until evenly combined.
Assemble: Spread ¼ cup enchilada sauce over the bottom of the prepared baking dish. Add the quinoa mixture and spread it into an even layer without pressing firmly. Drizzle the remaining ¼ cup enchilada sauce over the top and sprinkle with the remaining 1 cup cheese.
Bake: Cover loosely with foil and bake for 15 minutes. Remove the foil and bake for another 8–10 minutes, until the cheese is fully melted and the sauce bubbles around the edges. Rest for 10 minutes before serving.