ETFE cushion integrated transparent solar cell (EC-TSC) systems have gained more attention in recent years due to their lightweight structure, reduced material consumption, and renewable energy production. In this study, innovative EC-TSC systems are applied as the skylight for the atrium of a commercial building to replace the current PV glazing skylight. The environmental and economic sustainability of EC-TSC systems is investigated by applying life cycle assessment (LCA) and life cycle cost analysis (LCCA) in a cradle-to-cradle approach. LCA provides cumulative energy and greenhouse gas emissions to quantify environmental performance. LCCA considers the contribution of life cycle costs, building owner income, and social and environmental benefits to demonstrate economic viability and evaluate financial performance. A novel distributed allocation method is proposed to illustrate the impacts of recycling benefits across all life cycles. The results are compared with those of the previous PV glazing skylight. From the results, EC-TSC systems are shown to be more cost-effective and environmentally friendly than PV glazing skylights, provided the commercial product can realize the prospective physical characteristics. This paper demonstrates the significant potential of EC-TSC systems for building retrofitting in terms of economic and environmental performance, representing an important step toward supporting the transition of BIPVs to environmental and economic sustainability.