Pre-harvest application of inherently non-aflatoxigenic Aspergillus flavus strains is an effective biocontrol strategy to minimize aflatoxin contamination of agricultural commodities, but researchers still do not fully understand how A. flavus biocontrol strains effect control over toxigenic strains/species. In this study, we tested the potential for A. flavus volatile organic compounds (VOCs) identified from a previous study to serve as regulators of mycotoxin production. We exposed four Aspergillus strains (one non-aflatoxigenic and three aflatoxigenic) to five VOCs unique to aflatoxigenic A. flavus, and five VOCs unique to non-aflatoxigenic A. flavus, to study their impacts on growth as well as production of two mycotoxins: aflatoxin B1 and cyclopiazonic acid (CPA). We found that growth of the fungi was minimally impacted by VOCs. However, toxin production was greatly affected and highly variable between strains and VOCs. Two non-aflatoxigenic VOCs (2,3-dihydrofuran and decane) significantly reduced aflatoxin B1 levels and also completely inhibited CPA production. Our findings offer evidence that the mechanism of control, implemented by biocontrol strains, may involve production of one or more VOCs and offer potential to supplement current biocontrol efforts through post-harvest exposure to non-aflatoxigenic A. flavus VOC-related chemicals.