The increasing prevalence of Fusarium graminearum, a major causative pathogen of Fusarium head blight in cereal crops, leads to contamination of grain with mycotoxins, which necessitates the development of effective management strategies. This study investigated whether postharvest Blown-Arc plasma treatment could reduce F. graminearum and associated mycotoxins in field-infested grain. Postharvest Blown-Arc plasma treatment for 60 or 180 s was trialled to reduce Fusarium graminearum and deoxynivalenol (DON) mycotoxins in field-infested wheat grain. Changes in fungal components of the grain microbiome following the treatment were assessed using metabarcoding analysis of the nuclear ribosomal internal transcribed spacer gene region, and liquid chromatography mass spectrophotometry was used to measure changes in concentrations of the mycotoxins deoxynivalenol (DON), DON-3-glucoside (DON3-G) and 3-acetyl-DON (3-ADON). Fusarium spp. were the most common taxa in the grain over two seasons, with the relative abundance being higher in 2020 (72%) compared to 2021 (45%). Postharvest plasma treatment of field-infested grain for 60 or 180 s did not significantly lower Fusarium abundance. Alpha and beta diversity of the natural mycobiota in the grain were also unaffected. The concentrations of mycotoxins were not significantly different after the treatments, except that in the 2021 trial, the 180 s treatment caused a significant increase in DON concentration. We concluded that the postharvest plasma treatment used in this study did not reduce Fusarium contamination or the concentration of mycotoxins, DON, DON3-G and 3-ADON in field-infested grain. The results highlight the importance of using field-infested grain in experiments, as opposed to grain inoculated under laboratory conditions, which provides only superficial infection. This approach is crucial for accurately understanding the dynamics of treatment efficacy.