The aim of the study was to evaluate the influence not only of the year, but also of the three agronomic factors, namely pre-crops, soil tillage, and application of fungicides on the subsequent grain yield of winter wheat. The field trial was carried out at the Field Trial Station in Žabčice (South Moravia, Czech Republic), between 2014 and 2016, as part of a long-term field experiment focused on management of soil with livestock production. Winter wheat was grown after two pre-crops, namely alfalfa and silage maize. The soil was treated using three technologies, namely conventional tillage (CT) – ploughing to a depth of 0.24 m, minimum tillage (MT) – shallow loosening to a depth of 0.15 m, and no-tillage (NT) – direct sowing. In terms of fungicide treatment, two treatments were used and compared to a non-treatment variant. The obtained results suggest that the statistical significance was not found in the influence of the pre-crop. On the contrary, the influence of not only the year but also of the soil tillage technology and fungicide treatment was confirmed. Higher yields by 0.59 t/ha were achieved after shallow loosening and direct sowing as compared with after traditional ploughing and after application of fungicides. In addition, inconclusive influence of interaction between pre-crop and soil tillage as well as between soil tillage and fungicide treatment was also found.