Urban agriculture has emerged as an alternative to conventional rural agriculture seeking to foster a sustainable circular economy in cities. When considering the feasibility of urban agriculture and planning for the future of food production and energy, it is important to understand the relationships between energy flows throughout the system, identify their strengths and weaknesses, and make suggestions to optimize the system. To address this need, we analyzed the energy flows for growing tomatoes at a rooftop greenhouse (RTG). We used life cycle assessment (LCA) to identify the flows within the supply chain. We further analyzed these flows using ecological network analysis (ENA), which allowed a comparison of the industrial system to natural systems. Going beyond LCA, ENA also allowed us to focus more on the relationships between components. Similar to existing ENA studies on urban metabolism, our results showed that the RTG does not mimic the perfect pyramidal structure found in natural ecosystems due to the system's dependency on fossil fuels throughout the supply chain and each industry's significant impact on wasted energy. However, it was discovered that the RTG has strong foundational relationships in its industries, demonstrating overall positive utility; this foundation can be improved by using more renewable energy and increasing the recycling rates throughout the supply chain, which will in turn improve the hierarchy of energy flows and overall energy consumption performance of the system.