One of the saprophytic fungi that contaminates crops with carcinogenic aflatoxins is Aspergillus flavus. During pre-harvest and post-harvest, microbial produced bioactive compounds are regarded to be efficient biocontrol strategies for preventing contamination caused by foodborne pathogens and mycotoxins. The inhibitory effects on Aspergillus flavus of volatile organic compounds (VOCs) generated by Bacillus subtilis CL2 and the synthetic volatile 2,3-butanedione were investigated in this study. The results showed that strains CL2 and 2,3-butanedione reduced the disease severity caused by A. flavus infestation and suppressed the generation of A. flavus spores on peanut kernels under storage circumstances. Scanning electron microscopy revealed severely deformed conidia and hyphae of A. flavus after exposure to various doses of 2,3-butanedione. The cell content release and ergosterol content revealed that 2,3-butanedione harmed both the A. flavus cell wall and cell membrane. In conclusion, A. flavus is effectively inhibited by B. subtilis CL2 and its metabolic product 2,3-butanedione during peanut preservation. This research will look for novel strategies to use microbial and bioactive chemicals to combat fungal diseases in food and grain storage.