The fungi of the genus Fusarium cause Fusarium head blight (FHB), a devastating disease that reduces grain yield and quality. They also produce mycotoxins which may pose a serious threat to human and animal health. This study investigated the effects of NPK fertilisation, foliar application of Cu, Zn, and Mn, applied separately and in combination, and of the Nano-Gro® organic growth stimulator on the occurrence of FHB in cultivar Dańkowskie Diament rye based on the mycological analysis of kernels and on the concentrations of Fusarium mycotoxins in grain. The severity of FHB caused by seven species of the genus Fusarium was influenced by weather conditions in the analysed growing seasons. The applied fertilisation and the Nano-Gro® organic growth stimulator exerted varied effects on FHB development and the biosynthesis of Fusarium mycotoxins (deoxynivalenol, nivalenol, zearalenone and fumonisins) in grain. The greatest reduction in deoxynivalenol and nivalenol concentrations was noted in 2013, and the levels of moniliformin were lower in treated samples than in absolute control (untreated) samples in both years of the study. The severity of FHB positively correlated with the concentrations of zearalenone, deoxynivalenol, nivalenol, and moniliformin in the grain samples. Greater accumulation of ergosterol was noted in the rye grain harvested in 2013 than in 2012, and fertiliser treatment led to higher ergosterol concentrations than did control treatment.