Mycotoxin accumulation during the malting of wheat and barley grain causes millions of dollars in annual losses for the U.S. malting and brewing industry. This research investigates the use of biofumigant treatments from plant derived metabolites to reduce grain Fusarium contamination and mycotoxin production during malting. Defatted seed meals from five glucosinolate-containing members of the Brassicaceae Family: Brassica juncea, Brassica carinata, Lepidium sativum, Sinapis alba, and Thlaspi arvense were used to fumigate inoculated wheat and barley. We found that naturally produced gaseous allyl isothiocyanate was able to control Fusarium graminearum growth and mycotoxin contamination without harming wheat or barley germination. Treatment of Fusarium contaminated barley with volatiles from defatted Brassica juncea, in simulated malting conditions, completely prevented mycotoxin accumulation. No residual isothiocyanates were detected on the malted barley post kilning. This research demonstrates an alternative valorization of Brassicaceae seed meal byproducts as potent inhibitors of fungal contamination during malting.