This work was conducted to study the efficacy of pre-harvest spraying of soybean plants with some organic compounds [salicylic, succinic, oxalic, ascorbic acids and ethylenediaminetetraacetic acid (EDTA)] and some nanoparticles (NPs) e.g. Copper oxide (CuO), zinc oxide (ZnO) and magnesium oxide (MgO) for their antifungal activities against aflatoxins (AFs) producing fungi; Aspergillus flavus and A. parasiticus (A. flavus group) and AFs production after one year of storage. Laboratory and field trials were conducted at Etay El-Baroud Agricultural Research Station, El-Beheira governorate, Egypt, on soybean (Glycine max L.) cultivar Giza 21 during season 2017. The organic compounds were used at the concentrations of 25, 50, 75 and 100 mg/ml and NPs at the concentrations of 2.5, 5.0, 7.5 and 10 mg/ml. Generally, the radial growth inhibition increased with increasing the organic compounds and NPs concentrations. Soybean plants sprayed three times at bloom stage with organic compounds at 100 mg/ml and NPs at 10 mg/ml individually caused an increase in the weight of 100 seeds (g), a decrease in the disease incidence (%) and an increase in the seeds total protein content (%). The increment in seeds total protein content ranged between 53.2–2.87% compared with untreated control. After harvest (zero time), the organic compounds exhibited their reducing effect on AFs levels (B1, B2, G1 and G2) in seeds in the following order; EDTA< ascorbic acid< oxalic acid< salicylic acid< succinic acid with averages of 6.02, 9.00, 13.27, 29.92 and 31.46 ng/g, respectively. Also, examined NPs exhibited their reducing effect of AFs in the following order: CuO< MgO< ZnO with averages of 19.33, 42.87 and 58.57 ng/g, respectively. Under storage condition (95% relative humidity and 35 °C) for one year, the residual levels of AFs in artificially infected seeds and in non-infected seeds were non-detectable for B1, G1 and G2. However, oxalic acid treatment induced B2 generation (11.74 ng/g; average) in infected seeds and CuONPs induced generation (6.17 ng/g; average) in noninfected seeds.