The study is directed to establish the minimizing effects of Syzygium aromaticum, Ocimum sanctum, and Cananga odorata essential oils on the growth and ochratoxin A (OTA) level of Aspergillus ochraceus and Penicillium verrucosum in maize grains. S. aromaticum essential oil (SAEO), O. sanctum essential oil (OSEO), and C. odorata essential oil (COEO) were extracted by hydro-distillation technique, and a total of 50, 44, and 48 chemical constituents were identified by gas chromatography-mass spectrometry (GC-MS), respectively.The SAEO and OSEO belong to the chemotype of eugenol, whereas, COEO was found to be the chemotype of thymol, limonene, and α-ylangene. The antifungal activity of essential oils (EOs) was determined by the micro-well dilution technique. The SAEO showed superior antifungal activity compared to OSEO, COEO, and synthetic antifungal agent nystatin, and its minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) values against A. ochraceous and P. verrucosum were noticed as 1251 ± 42.32 and 1878 ± 28.47 µg/mL, and 0815 ± 22.69 and 1146 ± 51.19 µg/mL, respectively.The antifungal mechanism of EOs was unveiled by assessing the intracellular reactive oxygen species (ROS), ergosterol content, and membrane integrity. The antifungal investigations found that EOs caused fungal mortality by increasing the intracellular ROS, depleting ergosterol synthesis, and distracting membrane integrity. Finally, antifungal and antimycotoxin activity of EOs was demonstrated in maize grains. The SAEO, OSEO, and COEO have reduced the complete fungal growth and OTA level of A. ochraceous and P. verrucosum correspondingly at 2500 and 2500, 3500 and 2500, and 3500 and 3500 µg/g in maize. The EOs could act as natural antifungal agents; protect foodstuffs from fungal infection and mycotoxins during storage.