Preheat the oven to 400º F.
In small bowl, whisk together the olive oil, chipotle peppers, adobo sauce, brown sugar, smoked paprika, cumin, oregano and salt.
Add the bell peppers, shallots and garlic to a large baking dish. Toss the vegetables with 2 tbsp of the marinade you just made. Bake for 25-30 minutes or until the peppers have softened.
Meanwhile, rub the remaining marinade over the cod filets to coat and set aside.
Remove the peppers from the oven and stir. Nestle in the cod filets and return to the oven to bake for another 10-12 minutes, until the fish is cooked through.
Squeeze over the lime juice and serve immediantly with fresh cilantro, cooked quinoa, black beans and avocado.