Rinse the quinoa under cold water in a fine-mesh strainer. In a medium pot, combine 1 cup of quinoa with 2 cups of water. Bring to a boil, then reduce heat to low, cover, and simmer for about 15 minutes or until the quinoa is fluffy and water is absorbed. Remove from heat and set aside.
In a large skillet, heat 3 tablespoons of olive oil over medium heat. Add the sliced red onion and peppers. Sauté for about 5-7 minutes, or until the vegetables are tender and slightly caramelized.
Stir in the crushed chipotle chili flakes, chili powder, oregano, cumin, garlic powder, salt, and black pepper. Cook for an additional 1-2 minutes until the spices are fragrant.
In a large bowl, combine the cooked quinoa, sautéed vegetables, crushed tomatoes, and white beans. Mix well to ensure everything is evenly incorporated.
Pour the quinoa mixture into your prepared casserole dish. Spread it out evenly.
Top the mixture with the shredded Colby-Jack cheese. Cover the dish with aluminum foil and bake in a preheated oven at 375°F (190°C) for 25 minutes. Remove the foil and bake for an additional 10-15 minutes, or until the cheese is melted and bubbly.
Once out of the oven, let the casserole cool for a few minutes. Garnish with diced avocado, tomato, cilantro, and red onion if desired. Serve warm and enjoy the colorful flavors!