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Solar radiation transmissivity in greenhouses is a key property largely determined by covering materials. This study compared tomato crop yields and their environmental performance of a polycarbonate rooftop greenhouse with alternative covering materials displaying higher solar transmissivity and lifetime performance. An integrated approach using experimental data with structural, energy modeling was used to model average lifetime crop productivities. At building functional unit (per m2·year), impacts varied between -29.0% and +24.0% compared to the current polycarbonate. Lifetime transmissivities improved up to 20.5% (4 mm-antireflective glass), leading to +46.6% of tomato yields (19.9 ± 2.2 kg/m2), and up to -33.9% of environmental impacts. Ethylene tetrafluoroethylene 60 μm-film resulted in 19.2 ± 2.3 kg tomatoes/m2 but improved environmental performance up to 41.7%. These results demonstrate the importance of employing integrated and life-cycle approaches to combine multiple trade-offs and dynamics within environmental assessments of greenhouse crops. The results are intended to contribute to improving greenhouse cultivation and sustainability.