Wheat, a strategic global agricultural product, is prone to contamination by hazardous fungi and toxins, with aflatoxin being particularly prevalent and perilous. This study aimed to evaluate the efficacy of cold plasma in deactivating Aspergillus flavus (A.f.) and Aspergillus parasiticus (A.p.), as well as aflatoxins in wheat grains, offering an alternative to conventional chemical and thermal treatments. Wheat grains inoculated with fungi were subjected to humid air cold plasma at four power levels (5.39, 6.88, 8.98, and 10.88 W) and three plasma exposure periods (2, 6, and 12 minutes). Post-plasma treatment, Aflatoxin concentrations were analyzed using HPLC, while modified Gompertz and Baranyi and Roberts’ mathematical models were employed to study the growth kinetics of A.f. and A.p. species. Findings revealed that samples treated with 10.88 W power for 12 minutes exhibited a substantial reduction of 64%, 41%, 59%, 40%, and 61% in B1, B2, G1, G2 aflatoxins, and total aflatoxin, respectively. Additionally, plasma led to a 78.74% and 68.57% reduction in the growth of A.f. and A.p. fungi, respectively. Notably, plasma induced a fungal inhibitory effect by prolonging the lag time and decreasing the growth rate. These results underscore the significant potential of cold plasma as a capable technique for fungal inactivation and the emerging disinfection of contaminated wheat grains.