Controlled environment agriculture (CEA), specifically advanced greenhouses, plant factories, and vertical farms, has a significant role to play in the urban agri-food landscape through provision of fresh and nutritious food for urban populations. With the push towards improving sustainability of these systems, a circular or closed-loop approach for managing resources is desirable. These crop production systems generate biowaste in the form of crop and growing substrate residues, the disposal of which not only impacts the immediate environment, but also represents a loss of valuable resources. Closing the resource loop through composting of crop residues and urban biowaste is presented. Composting allows for the recovery of carbon dioxide and plant nutrients that can be reused as inputs for crop production, while also providing a mechanism for managing and valorizing biowastes. A conceptual framework for integrating carbon dioxide and nutrient recovery through composting in a CEA system is described along with potential environmental benefits over conventional inputs. Challenges involved in the recovery and reuse of each component, as well as possible solutions, are discussed. Supplementary technologies such as biofiltration, bioponics, ozonation, and electrochemical oxidation are presented as means to overcome some operational challenges. Gaps in research are identified and future research directions are proposed.