Fungi and their toxins have an impact on the hygienic standards and market value of corn (Zea Mayas L.) in Burkina Faso. Though effective, other pesticides have been shown to be harmful. This study aims to aid in the management of corn diseases by assessing the effectiveness of bio-fungicide formulations. In this study, the blotter method was used to assess the antifungal activity at doses of 0.5% (5 g/kg) and 1% (10 g/kg) of powdered formulations of Cymbopogon giganteus (F1) and Eucalyptus camaldulensis (F2) essential oils on the fungal flora of a corn sample. Untreated controls were also observed. The results of this study demonstrated that Aspergillus flavus and Aspergillus parasiticus, which could produce aflatoxin, were more susceptible to the 0.5% dose at F1 than at F2. Though Aspergillus niger and Rhizopus sp. were resistant to 0.5% of F1 and 0.5% of F2, while Fusarium sp. was resistant to 0.5% of F1. All of the above fungi were vulnerable to 1% of F1 and F2. Therefore, these two formulations could be utilized successfully to combat the decline in the hygienic, nutritional, and market value of corn in Burkina Faso caused by aflatoxin contamination and other toxins produced by these fungi. However, it would be important to evaluate the synergistic effect of these biofungicide formulations in situ and on a large scale.