Worldwide growing demand for food, alongside limited resources and accelerating environmental changes, suggests that future global food security may rely at least partially on unconventional land and production systems, such as built infrastructure located in desert areas. This paper analyses the environmental footprints (water, soil, carbon, material, solid waste, and ecological) of a tomato production system in passive greenhouses, a low-tech growing structure with no artificial heating or cooling. We collected data from 10 farms in the hyper-arid region of the Central Arava, Israel. Our analysis covers the four stages of production up to the overseas export destination and investigates the system's direct and indirect biophysical interactions. The average footprint of a ton of tomatoes is 1,040 kg/t (Material footprint), 94 m3/t (Water footprint), 72 m2/t (Land footprint), 952 kgCO2eq/t (Carbon footprint), 442 kg/t solid waste (SWF) and 243 gha/t (Ecological footprint). Our results indicate that the environmental hotspots can be attributed to universal factors–water production, fossil energy, fertilizers, structures, and road transport, alongside case-specific elements–soil, evaporation, location and the human-factor. Some differences were found when examining the full range of footprints within farms. No correlation was found between the farm's yields and materials inputs or carbon footprint, pointing to the human factor. We discuss the advantages and limitations of the local production system and proposed some improvement strategies.