Certain soils promote crop health because they are pathogen-suppressive (i.e., fungistatic) or disease-suppressive, but the effect of soil management on these properties is not fully understood. Here, we tested the hypothesis that manure could favor fungistasis by screening 26 manured or non-manured wheat fields from Serbia for their ability to control survival/growth of the fungal plant pathogen Fusarium graminearum Fg1. Quantitative PCR showed that the pathogen grew after inoculation in all 26 autoclaved soils. In absence of autoclaving, the pathogen was stable or grew in 16 soils (37 % manured) but declined in the 10 others (70 % manured). For most soils, there was no significant link between soil chemistry and fungistasis, except with Mionica in western/central Serbia. Mionica soils MI2 and MI3, which had received manure, exhibited higher levels of organic matter and potassium compared with soils MI4 and MI5, which had not received manure and were non-fungistatic. Using Mionica soils, we then tested the hypothesis that fungistatic (manured) soils rather than non-fungistatic (non-manured) soils would protect wheat from F. graminearum disease. Indeed, fungistatic soils were suppressive to wheat damping-off. Non-fungistatic soil MI4 was conducive, as expected, but non-fungistatic soil MI5 turned out to be suppressive. Metabarcoding showed that the structure of prokaryotic and fungal rhizosphere communities depended mostly on field location, with a significant effect of F. graminearum inoculation. In conclusion, our findings show that certain farming practices (here, manure amendments) may promote soil fungistasis towards F. graminearum. However, both fungistatic and non-fungistatic soils can be suppressive to F. graminearum disease in wheat, and their differences in rhizosphere microbiota suggest different phytoprotection mechanisms.