The research presented in this paper embraces a biophysical, materials flow analysis approach, to quantify various direct and indirect environmental interactions of bell peppers grown in the Israeli Arava desert region. The study examines the material flows of one metric ton of bell peppers grown in two types of structures, greenhouses and net-houses, throughout its life-cycle, from “cradle to port” (at key export destinations). It examines materials, land, water and energy inputs, and solid waste and GHG emissions through three stages (1) pre-cultivation including the production of raw materials; (2) cultivation and packaging; (3) post-cultivation, including shipping and waste management. The research found that while there were small differences between the structures themselves, there were major differences between the production-stages. On average, the production of 1 ton of bell peppers in the region (average of the two structures) uses 691 kg of materials, an area of 131 m2, and 280 m3 of water. It generates an average of 712 kg solid waste and 1156 kg CO2e. Overall, 21% (205 kg) of the materials were used during the pre-cultivation stage, 67% (643 kg) during cultivation and 12% (118 kg) during the post-cultivation stage. The highest CO2e emissions component of both growing systems is related to the pre-cultivation stage, i.e., production of raw materials (approximately 45%), followed by the cultivation stage (about 38%) and post-cultivation, mainly transportation (17%). The analysis identified the biophysical strengths and weaknesses of each phase, it also indicates possible alternatives for reducing environmental impact, including implementation of select technologies, and points out the influence of societal-communal and economic characteristics and the need for greater investment in the role of public policy.