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Fusarium head blight (FHB) is a devastating fungal disease of small-grain cereals that causes significant yield losses and mycotoxin contamination, diminishing food and feed safety worldwide. In contrast to wheat, little is known about the agricultural practices that influence FHB and Fusarium mycotoxins in barley. Thus, a nationwide survey was conducted across Switzerland for harvest samples in 2016 and 2017, accompanied with a questionnaire to obtain information about the agricultural practices in each barley field. In total, 253 grain and 237 straw samples were analyzed. In both years, F. graminearum was the predominant Fusarium species in grains followed by F. avenaceum and F. poae. Growing maize before barley was associated with increased amount of F. graminearum DNA in grains and straw as well as with elevated concentrations of deoxynivalenol in grains of barley. On the other hand, growing pasture before barley resulted in increased incidence of F. poae and concentration of numerous mycotoxins in grains (e.g., enniatins) and straw (e.g., beauvericin). Reduced tillage practices were linked to increased incidence of F. graminearum and deoxynivalenol content in grains and straw. In contrast, conventional tillage was linked to higher incidence of F. poae. Moreover, use of spring barley was associated with decreased amount of F. graminearum DNA in grains and straw, but increased incidence of F. poae and F. avenaceum. Use of the spring variety Eunova was linked to increased concentrations of several Fusarium mycotoxins in grains (e.g., enniatins and nivalenol). Furthermore, the application of strobilurin-based fungicides was associated with higher deoxynivalenol and beauvericin contents in grains. The application of plant growth regulators was associated with increased concentration of some Fusarium mycotoxins in grains (e.g., culmorin), while absence of growth regulators application was linked to elevated concentration of some other mycotoxins (e.g., nivalenol). We conclude that individual agricultural practices can suppress some FHB causing species and reduce the associated mycotoxins, but can promote others. Hence, integrated control measures combining numerous prevention and intervention strategies should be applied for the sustainable management of mycotoxins in barley.