The present evaluation aimed to synthesis and characterise the Pogostemon cablin essential oil encapsulated chitosan nanoemulsion (PCEO-CN) and evaluated its antifungal antimycotoxin and antioxidant activities. A total of twenty-six different chemical compounds were identified from P. cablin essential oil (PCEO), among which patchoulol (34.93%), α-bulnesene (17.76%) and α-guaiene (15.44%) were recorded as major components. The average size of PCEO-CN was 18.20nm. The PCEO-CN showed concentration-dependent broad-spectrum antifungal and antimycotoxin activities. The in vivo evaluation showed that PCEO-CN significantly protected maize seeds from mould-induced biodeterioration and aflatoxin B1 biosynthesis for up to 30days. The PCEO-CN significantly inhibits ergosterol biosynthesis and cellular integrities of A. flavus. Based on the present study, PCEO-CN could be used as a food preservative to control mould and mycotoxin contamination in stored maize. © 2021 Institute of Food Science and Technology.