The objective of this study was to examine the effect of treatment of Arabica green coffee beans with gaseous ozone (O3) for the control of ochratoxigenic fungi and ochratoxin A (OTA) contamination by Aspergillus westerdijkiae, A. ochraceus, and A. carbonarius during storage. Studies included (i) relative control of the populations of each of these three species when inoculated on irradiated green coffee beans of different initial water availabilities using 400 and 600 ppm gaseous O3 treatment for 60 min at a flow rate of 6 L−1 and on OTA contamination after 12 days storage at 30 °C and (ii) effect of 600 ppm O3 treatment on natural populations of green stored coffee beans at 0.75, 0.90, and 0.95 water activity (aw) or with additional inoculum of a mixture of these three ochratoxigenic fungi after treatment and storage for 12 days at 30 °C on fungal populations and OTA contamination. Exposure to 400 and 600 ppm O3 of coffee beans inoculated with the toxigenic species showed that there was less effect on fungal populations at the lowered aw (0.75). However, toxigenic fungal populations significantly increased 48 h after exposure and when stored at 0.90 and 0.95 aw for 12 days. All three species produced high amounts of OTA in both O3 treatments of the wetter coffee beans at 0.90 and 0.95 aw. Gaseous O3 (600 ppm) treatment of naturally contaminated green coffee beans had little effect on fungal populations after treatment, regardless of the initial aw level. However, after storage, there was some reduction (26%) observed in coffee at 0.95 aw. In addition, no fungal populations or OTA contamination occurred in the 0.75 and 0.90 aw treatments after exposure to 600 ppm gaseous O3 and storage for 12 days. It appears that under wetter conditions (≥0.90–95 aw) it is unlikely that fungal populations and OTA contamination of stored coffee beans, even with such high O3 concentrations would be controlled. The results are discussed in the context of potential application of O3 as an intervention system for stored coffee post-fermentation and during medium term storage and transport.