| Summary: | Substitution of organic with inorganic fungicides (phosphites, Phi) does not change the efficiency of fertilizer nitrogen (N<sub>f</sub>) in winter wheat. This hypothesis was tested in the 2016/2017 and 2017/2018 growing seasons. A two-factorial experiment with three phosphite variants (Cu–Phi, Mg–Phi, and Cu/Mg) and six plant protection methods (fungicides + Phi ⟶ reduced fungicide frequency + phosphite ⟶ phosphite). Grain yield decreased with increasing frequency of phosphites instead of fungicides. The decrease in yields was 3.6 t ha<sup>−1</sup> in the favorable 2016/2017 and 1.1 t ha<sup>−1</sup> in the dry 2017/2018. The primary reason for yield decrease in a given growing season was increased wheat infestation by pathogens. The direct cause was disturbances in the nitrogen status of wheat after flowering on treatments with a predominance of phosphites. The thousand grain weight (TGW) responded negatively to reduced fungicide application frequency. The critical stage in the assessment of pathogen pressure on wheat was the medium milk phase (BBCH 75). At this stage, indices of SPAD and leaf greenness together with indices of wheat infestation with pathogens allowed for a reliable prediction of both TGW and grain yield. It can be concluded that phosphites do not substitute organic fungicides in limiting pathogen pressure in winter wheat. Moreover, increased pressure of pathogens significantly reduces N<sub>f</sub> productivity.
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