Bring the quinoa and water to a boil in a small pot. Cover, reduce the heat to low and simmer for 15 minutes. Remove from the heat and let it stand, covered, for 5 minutes.
Meanwhile, heat the oven to 375°F (190°C). Arrange the pepper halves cut side up in a baking dish.
Heat the oil in a skillet over medium heat. Cook the onion for 5 minutes, then add the garlic, cumin and paprika and stir for 1 minute.
Add the beans, tomatoes, corn and salt and simmer for 5 minutes. Stir in the cooked quinoa and half the cheese.
Pack the filling into the pepper halves, mounding it slightly. Pour 1/4 cup of water into the bottom of the dish and cover with foil.
Bake for 25 minutes. Uncover, sprinkle with the remaining cheese and bake for 10–15 minutes more, until the peppers are tender and the cheese is golden.
Serve topped with cilantro and a squeeze of lime.