Chop the onion in half-moons. Grill the peppers and jalapeño on the open flame of your stove: Put the peppers directly on the flame, leave it there for 1-2 minutes until it is black, using tongs turn them so that it burns the skin on all sides, around 10 minutes. Remove and let them rest/steam on a closed plastic bag for 15 minutes. Wash the skin off under running water. Remove seeds and chopped the peppers into thin strips.
Mix peppers and onion in a bowl and sprinkle with the fajitas seasoning. Stir well.
In a baking dish with a diameter of 8′ or similar, combine the beans with the farro or quinoa. Stir. Place the shredded chicken on top. Sprinkle over half the cheese. Cover with the onion and peppers seasoned. Cover with foil and bake 30 minutes.
Uncover, place the rest of the cheese on top and cook 10 minutes more. Until bubbling and the cheese is melted.
Let stand 5 minutes before serving. Serve with sliced roasted jalapeño and chopped cilantro.