Low pressure cold plasma (LPCP) using air gases and sulfur hexafluoride (SF(6)) was developed and tested for anti-fungal efficacy against Aspergillus parasiticus on various nut samples. Artificially A. parasiticus contaminated hazelnuts, peanuts, and pistachio nuts were treated with air gases plasma and SF(6) plasma for up to 20 min duration. The sterilizing effect of LPCP on A. parasiticus was higher during the early treatment period than the later treatment period. Air gases plasma treatment for 5 min resulted in 1-log reduction of A. parasiticus and a further 5 min treatment resulted in additional 1-log reduction. SF(6) plasma application was more effective resulting in approximately a 5-log decrease in fungal population for the same duration. When effectiveness of plasma treatment against aflatoxins were tested, 20 min air gases plasma treatment resulted in a 50% reduction in total aflatoxins (AFB1, AFB2, AFG1, and AFG2), while only a 20% reduction in total aflatoxin was observed after 20 min SF(6) plasma treatment. In this study, a rapid, functional clean-up method for the elimination of aflatoxin producing fungus from shelled and unshelled nuts was investigated as a suitable fungal decontamination method.