The demand for wheat production is increasing and is associated with environmental effects. To sustain the increased demand, there is a need to find sustainable methods of wheat production. The choice of cropping system can significantly affect the environmental burden of agricultural production systems. This study presents the results of monitoring emission loads resulting from winter wheat cultivation under different cropping systems: organic unfertilized (ORG), organic fertilized (ORG-F), conventional unfertilized (CON), and conventional fertilized (CON-F). The system boundaries include all the processes from “cradle to farm gate” and the functional unit was 1 kg of wheat grain. The primary data were obtained from experimental field trials and secondary data from Ecoinvent v3.5, WFLDB, and Agri-footprint v5.0 databases. The results of this study are related to eight impact categories. The SimaPro 9.2.0.1 software and ReCiPe Midpoint (H) V1.13/Europe Recipe H were used for calculation. The results show that fertilized variants recorded higher environmental impacts compared to the unfertilized variants. The results indicate that ORG-F was more environmentally friendly compared to the CON-F variant at the expense of lower yields. Overall, ORG imposes the lowest environmental impact and is deemed to be more environmentally friendly.