Breeding of multi-resistant varieties to reduce yield loss due to disease damage and lodging, and reduction of input intensity are of high importance for a more sustainable cereal production. The aim of this study was to evaluate (i) yield reduction caused by diseases and lodging and (ii) impact of input intensity and soil fertility in cereal variety trials grown under two intensities. Intensity 2 was treated with and intensity 1 without fungicides and growth regulators. We applied multiple regression approaches based on mixed linear models. First, we estimated relative yield reduction in intensity 1 compared to intensity 2 as a function of severity scores of diseases and lodging. High yield reductions occurred in winter wheat and winter triticale, moderate in winter rye and winter barley and low in spring barley. The damage potential was highest for yellow rust, followed by brown rust, lodging and Septoria tritici blotch. Medium damage potential was identified for dwarf leaf rust and low for powdery mildew, Septoria nodorum blotch, Rhynchosporium as well as for stem and ear buckling. Second, differences in input intensity did not affect yield in intensity 2 across the range of nitrogen and fungicide application rates while higher yield occurred at higher growth regulator rates and soil fertility. Growth regulator was strongly related with higher yield in winter rye and winter barley, however in spring barley, a negative relation was found. Soil fertility showed the strongest yield impact in all crops.