Common pollutants in agricultural commodities include mycotoxins, produced by toxigenic fungi such as Fusarium and Aspergillus. Conventional techniques using chemical fungicides can pollute the environment and lead to fungicide resistance. Eco-friendly and sustainable alternatives are provided by endophytic fungi like Penicillium and Trichoderma. These fungi produce antifungal chemicals, induce systemic resistance against infections, and compete for resources. By utilizing the biocontrol capabilities of endophytic fungi, farmers can protect their crops from mycotoxin contamination and enhance food safety. To fully investigate the advantages of these helpful fungi and create useful agricultural applications, further study must be conducted.