It is widely accepted that urban agriculture provides multiple benefits to society. Rooftop greenhouses are a form of urban agriculture that takes advantage of urban resources (urban land, sunlight spaces) and waste flows (energy, nutrients) to provide food and other ecosystem services to cities. However, the integration of urban greenhouses within buildings is a complex issue that must be addressed in-depth. Compared to the well-known conventional greenhouses, the urban environment requires an assessment to later optimize greenhouse structures and covering materials. The aim of our study was to environmentally assess rooftop greenhouses and propose improving scenarios. Life cycle assessment was used to detect environmental hotspots and to evaluate different impact categories of an iRTG case study in the Barcelona area. Results showed that the greenhouse environment and ventilation design directly determine greenhouse structures and environmental impacts. Optimized strategies showed a potential reduction of up to 35% of the amount of structural steel used, while less improvement potential existed for covering materials (5%). Compared to conventional greenhouses, 1.6 times more steel and up to 8 times more energy were required to build the urban greenhouse in this study. The assessment revealed that these differences can be reduced by optimizing greenhouse structures to avoid a shift of material flows and environmental impacts from building urban greenhouses compared to conventional greenhouses. In turn, the assessment presented here provides guidelines on how to design and plan urban greenhouse constructions in future assessments. That will facilitate the incorporation of urban agriculture in cities based on consistent environmental assessments, ultimately contributing to the low-carbon future development of cities.