This research investigated the efficacy of gaseous ozone for the inactivation of Escherichia coli ATCC 25922 and NCTC 12900 strains in orange juice. Orange juice inoculated with E. coli (106 CFU mL− 1) as a challenge microorganism was treated with ozone at 75–78 µg mL− 1 for different time periods (0–18 min). The efficacy of ozone for inactivation of both strains of E. coli was evaluated as a function of different juice types: model orange juice, fresh unfiltered juice, juice without pulp, and juice filtered through 500 µm or 1 mm sieves. Fast inactivation rates for total reduction of E. coli were achieved in model orange juice (60 s) and in juice with low pulp content (6 min). However, in unfiltered juice inactivation was achieved after 15–18 min. This indicated that juice organic matter interferes with antibacterial activity of gaseous ozone. The effect of prior acid (pH 5.0) exposure of E. coli strains on the inactivation efficacy of ozone treatment was also investigated. There was a strain effect observed, where prior acid exposure resulted in higher inactivation times in some cases by comparison with the control cells. However, the overarching influence on inactivation efficacy of ozone was related to the pulp content. Generally, the applied gaseous ozone treatment of orange juice resulted in a population reduction of 5 log cycles.