Plastic and straw coverage (PC and SC) are often combined with fungicide application but their influence on fungicide entry into soil and the resulting consequences for soil quality are still unknown. The objective of this study was to investigate the impact of PC and SC, combined with fungicide application, on soil residual concentrations of fungicides (fenhexamid, cyprodinil, and fludioxonil), soil fungal biomass, mycotoxin occurrence, and soil organic matter (SOM) decomposition, depending on soil depth (0–10, 10–30, 30–60 cm) and time (1 month prior to fungicide application and respectively 1 week, 5 weeks, and 4 months afterwards). Soil analyses comprised fungicides, fusarium mycotoxins (deoxynivalenol, 15-acetyldeoxynivalenol, nivalenol, and zearalenone), ergosterol, soil microbial carbon and nitrogen, soil organic carbon, dissolved organic carbon, and pH. Fludioxonil and cyprodinil concentrations were higher under SC than under PC 1 week and 5 weeks after fungicide application (up to three times in the topsoil) but no differences were observed anymore after 4 months. Fenhexamid was not detected, presumably because of its fast dissipation in soil. The higher fludioxonil and cyprodinil concentrations under SC strongly reduced the fungal biomass and shifted microbial community towards larger bacterial fraction in the topsoil and enhanced the abundance and concentration of deoxynivalenol and 15-acetyldeoxynivalenol 5 weeks after fungicide application. Independent from the different fungicide concentrations, the decomposition of SOM was temporarily reduced after fungicide application under both coverage types. However, although PC and SC caused different concentrations of fungicide residues in soil, their impact on the investigated soil parameters was minor and transient (< 4 months) and hence not critical for soil quality.