Tomato is one of the most popular and consumed crops worldwide and its cultivation via hydroponic techniques is widespread. In this study, we evaluated the performance of an evolving management strategy through an iterative system design over 8 years in an integrated-rooftop greenhouse in Barcelona. Yield, solar radiation, water and nutrient consumption, and environmental impacts through Life Cycle Assessment were analysed. We hypothesized that improving irrigation management, partially substituting mineral fertilizers with recovered nutrients, and ensuring optimal solar radiation would enhance tomato productivity while reducing the environmental impact. The highest productivity was obtained in 2023 (49 g plant−1 day−1), in a cycle using 100 g plant−1 of struvite and in a cycle using mineral fertilization. The replacement of deteriorated polycarbonate sheets in 2023 increased greenhouse solar transmissivity and led to the highest productivity. Life Cycle Assessment impacts were mainly driven by crop yields, growing system characteristics, and energy required to power artificial lighting or nebulization systems, among other inputs. The lowest environmental impacts were obtained in the 2017 cycle (0.54 kg CO2 eq.) followed by the 2023 cycle (0.94 kg CO2 eq.), in which the highest yields were produced thanks to optimal solar transmissivity, dynamic fertigation, and/or struvite. The highest environmental impacts (3.84–12.05 kg CO2 eq.) were achieved in cycles with the lowest productivity (0.9–3.3 kg m−2) and in cycles using artificial lighting in the greenhouse (3.71 kg CO2 eq.) or in an indoor environment (7.07 kg CO2 eq.). Our findings demonstrate that statistically higher yields and environmental sustainability can be achieved by adopting struvite-based fertilization and regularly replacing the greenhouse covering material to ensure maximum light transmissivity. This research provides valuable and novel insights into optimizing tomato cultivation in rooftop greenhouses, achieving constant yields, and reducing the environmental footprints thus contributing to sustainable food production.