Fusarium head blight (FHB) is a fungal disease of cereals including wheat, which results in significant economic losses and reductions in grain quality. Additionally, the presence of Fusarium spp. results in productions of mycotoxins/metabolites, some of which are toxic in low concentrations. The liquid chromatography with tandem mass spectrometry (LC-MS/MS) method was applied to 216 wheat samples from field conditions diseased with FHB. Data obtained show that out of 28 metabolites detected, deoxynivalenol (DON), deoxynivalenol-3-glucoside (D3G), enniatin B (ENN B), enniatin B1 (ENN B1), culmorin, 15-hydroxyculmorin, and aurofusarin were the most prevalent mycotoxins/metabolites over three years (2014–2016). In 2014–2016, 100, 100 and 96% of the samples were contaminated with zearalenone (ZEN). Of the masked mycotoxins, D3G occurred at a high incidence level of 100% in all three investigated years. Among emerging mycotoxins, moniliformin (MON), beauvericin (BEA) and enniatins (ENNs) showed high occurrences ranging from 27 and 100% during three investigated years. Co-occurrence of Fusarium mycotoxins/metabolites was high and almost all were highly correlated to each other but their possible synergistic, additive, or antagonistic effects of toxicity, should be taken into consideration. Our results demonstrated that modified and emerging mycotoxins/metabolites contributed substantially to the overall contamination of wheat grains. To avoid disparagement, it is necessary to analyse these forms in future mycotoxin monitoring programs and to set their maximum levels.