Postharvest losses of wheat (Triticum aestivum) grains due to fungal infestation pose a serious challenge to food security and grain quality during storage. Wheat grains are highly susceptible to deterioration under higher temperature and moisture content along with suitable pH that favour microbial contamination. During study, collected stored wheat samples showed pH 6.58 and moisture content 13.86% that significantly correlating with increased fungal incidence. Dominant fungal contaminants isolated from wheat grains belonged to Aspergillus, Cladosporium, Penicillium, and Fusarium species. A total of 231 fungal isolates were recovered in which Aspergillus flavus (25.11%) exhibited highest relative density followed by Cladosporium sp. (18.61) and Aspergillus niger (13.85%), while, lowest relative density was found in Aspergillus sydowii (1.73%) followed by Fusarium sp. (3.03%). The minimum inhibitory concentration (MIC) of Eucalyptus citriodora essential oil against Aspergillus flavus was recorded at 9.0 µL/mL and also exhibited broad fungitoxic spectrum. The findings suggest that ECEO is an effective, eco-friendly botanical fungicide for the management of fungal infestation in stored wheat grains.