Urban food systems need remedies due to the global rise of food insecurity. Aquaponics has emerged as a circular agricultural mode to shape edible cities and features multiple food–water–energy (FWE) nexus. Here we provide a generalizable methodology and framework to capture the FWE nexus flows of aquaponics systems within city jurisdiction. To test the framework in Beijing, China, we offer an evidence-based tradeoff analysis of urban rooftop aquaponics (RA) and ground aquaponics (GA) from a FWE nexus perspective. The results show that urban aquaponics performs well in terms of water efficiency, which saves 42%–44% of water consumption than traditional greenhouses (TG) during the on-farm stage, but generates 2.3–3.0 times higher energy consumption and 1.1–2.1 times more carbon emissions. “From farm to table” aquaponics helps decrease 14%–44% of the energy, water, and carbon impacts during the off-farm stage. With diversely optimized strategies for renewable electricity, fish food, infrastructure materials, and recycling actions, urban aquaponics can hopefully reduce energy consumption and carbon emissions by 80%–85% in the on-farm stage. In addition to greenhouse agriculture, utilizing a total of 155 km² of RA and GA potential areas could increase urban vegetable self-sufficiency by 15%, and avoid 82% of the energy, water, and carbon footprints during upstream food supply chains beyond cities. Our findings could provide policy insights for urban stakeholders to create edible landscapes by integrating RA and GA, and thus direct resilient and sustainable agricultural transformation.