Empirical data is key to anticipate the impact of climate change on cropping systems and develop land management strategies that are sustainable while ensuring food security. Here, the combined effects of projected increases in temperature, atmospheric CO2-concentrations, solar irradiation and altered precipitation patterns on winter wheat cropping systems were investigated using an Ecotron. Experimental plant-soil systems were subjected to three different climatic conditions representing a gradient of ongoing climate change implementing the weather patterns of the years 2013, 2068, and 2085 respectively. The wheat plants were grown in two differentially manged agricultural soil types: one with long-term low organic matter (OM) inputs and the other one with long-term high OM inputs. In the low OM system, the risk for plant diseases and nitrate leaching was increased, but it outperformed the high OM system with higher yields and lower CO2-emissions. Developing high-yielding cropping systems leveraging the CO2-fertilisation effect without sacrificing environmental health will therefore require further refined of management practices to improve nutrient cycling and reduce greenhouse gas emissions. One possibility is adapting crop rotations and cover crops to the shorter wheat cycle observed in the future climates to replenish soil nutrients and break disease cycles. Further, in both here studied soil types the wheat plants developed natural coping mechanisms against environmental stressors, such as enhanced root growth and increased levels of proline and silicon. Unravelling the molecular mechanisms that trigger such inherent plant defences is a further interesting target for breeding future crops.