Given the environmental footprints of the conventional agriculture, it is imperative to test and validate alternative production systems, with lower environmental impacts to mitigate and adapt our production systems. In this study, we identified six production systems, four in Italy and two in Denmark, to assess the environmental footprint for comparison among the production systems and additionally with conventional production systems. SimaPro 8.4 software was used to carry out the life cycle impact assessment. Among other indicators, three significantly important indicators, namely global warming potential, acidification, and eutrophication, were used as the proxy for life cycle impact assessment. In Italy, the production systems compared were silvopastoral, organic, traditional, and conventional olive production systems, whereas in Denmark, combined food and energy production system was compared with the conventional wheat production system. Among the six production systems, conventional wheat production system in Denmark accounted for highest global warming potential, acidification, and eutrophication. In Italy, global warming potential was highest in traditional agroforestry and lowest in the silvopastoral system whereas acidification and eutrophication were lowest in the traditional production system with high acidification effects from the silvopastoral system. In Italy, machinery use contributed the highest greenhouse gas emissions in silvopastoral and organic production systems, while the large contribution to greenhouse gas emissions from fertilizer was recorded in the traditional and conventional production systems. In Denmark, the combined food and energy system had lower environmental impacts compared to the conventional wheat production system according to the three indicators. For both systems in Denmark, the main contribution to greenhouse gas emission was due to fertilizer and manure application. The study showed that integrated food and non-food systems are more environmentally friendly and less polluting compared to the conventional wheat production system in Denmark with use of chemical fertilizers and irrigation. The study can contribute to informed decision making by the land managers and policy makers for promotion of environmentally friendly food and non-food production practices, to meet the European Union targets of providing biomass-based materials and energy to contribute to the bio-based economy in Europe and beyond.