In this study, 14 fungal isolates associated with symptomatic onion samples collected from different counties of Sohag Governorate showing neck rot disease were isolated and identified as Botrytis allii Munn (12 isolates) and 2 isolates of B. cinerea Pers. Pathogenicity tests carried out in the greenhouse showed that only the isolates of B. allii were pathogenic to onion plants and caused identical neck rot symptoms among all tested fungal isolates. However, B. allii isolates exhibited different levels of virulence. Isolate No. 9 of B. allii was the highest pathogenic one. In vitro, the influence of carbon, MgO, and ZnO nanoparticles was tested at 0.1, 0.2, and 0.3 mM on mycelial linear growth and biomass of B. allii. Results obtained showed that all tested nanomaterials significantly reduced the mycelial linear growth and biomass at all tested concentrations. The nano MgO at 0.3 mM caused the high inhibitory effect followed by nano ZnO, where they highly reduced mycelial linear growth and biomass compared to the untreated controls. In greenhouse and field experiments, the MgO and ZnO nanoparticles at 0.3 mM highly reduced the disease incidence and severity compared with the control of untreated plants. Moreover, the MgO and ZnO nanoparticles at 0.3 mM highly reduced the neck rot incidence and the decline in bulb weight of onion due to infection with B. allii during storage. Therefore, this study reports that the MgO and ZnO nanoparticles are eco-friendly alternative approaches for suppressing neck rot disease on onion in the field and storage.