This study investigated the effect of chitosan combined with essential oils (cinnamon, lemon, and oregano, respectively) as edible films against the growth of three important disease-causing pathogens of pomegranate (Botrytis sp., Penicillium sp., and Pilidiella granati). Essential oils (EOs) were characterised by gas chromatography analysis and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). In vitro antifungal activity of the EOs against Botrytis sp., Penicillium sp., and Pillidiella granati was conducted on agar media inoculated with fungal spores using the inverted lid and direct contact with agar techniques. Cast films were prepared from chitosan of different (low, medium, and high) molecular weights (Mw), and assessed for use as biodegradable packaging material. Thereafter, chitosan films (medium Mw) were used in combination with 0, 10, 50 or 100gL−1 concentrations of EOs (cinnamon, lemon, and oregano) for in vitro investigation. The use of ATR-FTIR effectively discriminated the EOs based on the energy levels of the atomic bond vibrations present, as indicated by their characteristic absorption peaks. Based on GC–MS analysis of the selected EOs, 35 volatile compounds belonging to eight different chemical classes were tentatively identified. In addition, differences in chitosan Mw were found to have significant influence on the film functional properties such as colour, thickness, contact angle, and tensile strength. Based on in vitro investigation, chitosan-oregano or −cinnamon EO films with the concentration of 10gL−1 exhibited complete inhibitory effect against all three pathogens. Maximum inhibitory effects of chitosan-lemongrass films was dependent on EO concentration, with P. granati, Botrytis sp., and Penicillium sp. inhibited completely at 10, 50, and 50gL−1, respectively. Antifungal in vivo study on pomegranate fruit artificially inoculated with Botrytis sp. and treated with chitosan-oregano EO (emulsions and films), showed that both treatment methods inhibited Botrytis sp. growth. However, the inhibitory effect was higher for fruit directly dipped into the chitosan-EO emulsions as opposed to samples exposed to vapour contact via the films. This study showed that chitosan-EOs applied as edible coatings or casted films can be used to control postharvest fungal pathogens associated with pomegranate fruit.