Nowadays, it has been difficult to control exposure of humans to fungal toxic metabolites, because these metabolites naturally occur in the environment. Therefore, the use of natural compounds like essential oils, besides biocontrol than that of synthetic products, can be a good alternative for addressing this problem. Seven fungal species belonging to four genera were isolated from ten samples of wheat grains randomly collected from Jazan Region, Saudi Arabia, with using the direct plating technique. Because Aspergillus niger was the most distributed and the most frequent fungus in wheat grains, therefore their identification was confirmed by PCR and tested for production of malformin A, malformin C, and maltoryzine in synthetic and natural media, besides using safe additive essential oils (EOs) for controlling these toxic metabolites production. Productivities of malformin A, malformin C, and maltoryzine were 13.4 ± 0.00, 9.6 ± 0.05, and 0.37 ± 0.00 μg/l synthetic medium compared with 17.4 ± 0.18, 11.9 ± 0.05, and 0.49 ± 0.01 μg/l natural medium, respectively. Malformin A, malformin C, and maltoryzine production was suppressed by neem oil, where production inhibition percent were 45.98, 47.89, and 51.01 on natural compared to 29.85, 29.16, and 35.13% on synthetic media for malformin A, malformin C, and maltoryzine, respectively, at 7.50% (v/v) neem oil. With using oregano EO 7.50% (v/v), inhibitions of malformin A, malformin C, and maltoryzine production were 44.77, 46.88 and 67.57% on synthetic growth medium, and 45.98, 38.65 and 51.02%, respectively, on natural medium. A weak remarkable reduction of these toxin syntheses was observed with using fenugreek EO compared with the other used oils.