In a large bowl, whisk together cilantro, olive oil, lime juice, garlic and lime zest. Add chicken, and toss to coat. Let marinate while you prep the remaining ingredients (about 10 to 15 minutes).
Remove seeds and core from bell peppers, then cut into thin strips. Remove ends of the onion, cut in half then slice into thin strips. Add vegetables to a parchment-lined baking sheet. Add chicken and fajita seasoning, and toss to coat.
Bake 18 to 20 minutes, tossing halfway through, or until chicken is cooked through. Switch oven setting to broil and broil for 3 to 4 minutes until edges are slightly crispy. Remove from oven, and sprinkle cheese over chicken-vegetable mixture. Return to oven and broil an additional 2 to 3 minutes or until cheese is melted and begins to bubble.