The effectiveness of ozone for the decontamination of Escherichia coli and Bacillus cereus in kernels, shelled and ground pistachios was investigated. Pistachios were inoculated with known concentrations of E. coli and B. cereus. Pistachio samples were exposed to gaseous ozone in a chamber at three different concentrations (0.1, 0.5 and 1.0 ppm) for various times (0–360 min) at 20 °C and 70% relative humidity. The effectiveness of ozone against E. coli and B. cereus increased with increasing exposure time and ozone concentration. The physico-chemical properties including: pH, free fatty acids and peroxide values, colour and fatty acid composition of pistachios did not change significantly after the ozonation treatments, except for the peroxide value of ground pistachios ozonized at 1.0 ppm for 360 min. Ozone concentration of 1.0 ppm was effective in reducing E. coli and B. cereus counts in kernels and shelled pistachios, while ozone concentrations <1.0 ppm were found to be appropriate in reducing the number of both bacteria in ground pistachios without having any change in their physico-chemical properties.