Andean blackberries are highly perishable due to their susceptibility to water loss, softening, mechanical injuries, and postharvest diseases. In this study, the antimicrobial efficacy of gaseous ozone against spoilage (mesophiles, psychrotrophs, and yeasts and molds) and pathogenic (E. coli, S. enterica, and B. cinerea) microorganisms was evaluated during 10 days of storage at 6 ± 1 °C. Respiration rate and mass loss were also determined. Ozone was applied prior to storage at 0.4, 0.5, 0.6, and 0.7 ppm, for 3 min. The best results were observed with the higher ozone dose, with initial maximum reductions of ~0.5, 1.09, and 0.46 log units for E. coli, S. enterica, and B. cinerea, respectively. For the native microflora, maximum reductions of 1.85, 1.89, and 2.24 log units were achieved on day 1 for the mesophiles, psychrotrophs, and yeasts and molds, respectively, and this effect was maintained throughout storage. In addition, the lower respiration rate and mass loss of the blackberries ozonated at 0.7 ppm indicate that this treatment did not induce physiological damage to the fruit. Gaseous O3 could be effective in maintaining the postharvest quality of blackberries throughout refrigerated storage but higher doses could be advisable to enhance its antimicrobial activity.