In a medium pot, combine the quinoa with 1 cup water. Cook over medium heat until water is absorbed, about 15 minutes. Set aside.
Heat the olive oil over high heat in a large pot. Add the onion and cook for approximately 5 minutes. Stir in garlic, jalapeño, and capsicum and cook for about 10 minutes until tender.
Add the vegetable stock, black beans, kidney beans, corn and tomatoes. Stir through the cooked quinoa. Season with chilli powder, dried oregano, cumin, salt, and pepper. Simmer for at least 30 minutes on low. Serve warm.