Nanoemulsions (NEs) of two antimicrobial formulations (AF-1 and AF-2), a mixture of essential oils and citrus extracts, were prepared by microfluidization. For optimization, a central composite design was used to ascertain the effect of independent variables (pressure, number of cycles, and emulsifier concentration) on the physical properties of NEs [i.e., droplet size (DS), polydispersity index (PDI), zeta potential (ζ), and encapsulation efficiency (EE)] and compare with coarse emulsion. The optimized AF-1 and AF-2 values had DS of 116 and 40 nm, PDI of 0.17 and 0.2, ζ-potential of 49 and 32.3 mV, and EE of 77 and 79%, respectively. The microbicidal properties of the NEs against Escherichia coli O157:H7, Salmonella Typhimurium, Aspergillus niger, Penicillium chrysogenum, and Mucor circinelloides were significantly (P ≤ 0.05) higher than the coarse emulsion. The NEs of both AFs were incorporated into a chitosan-based (CH) film. In situ tests with rice using bioactive CH-based nanocomposite films (BCHNF) reinforced with cellulose nanocrystals (CNCs) were tested against selected bacteria and fungi with and without γ-irradiation (750Gy) and stored for eight weeks. The BCHNF alone reduced 50–71 % of bacterial and fungal growth compared to the controls, while the combined action of γ-irradiation and films reduced 73–93 % of the tested microbial growth compared to untreated controls. Incorporation of CNC into BCHNF demonstrated a predictable pattern of slower release of active components (32–39 %) over the eight week period compared to the bioactive films without CNC. The sensory qualities of rice did not change significantly after BCHNF treatments.