Fungal diseases developing on apples during storage can lead to substantial fruit losses. Pathogens infecting apples on the orchards and developing during storage are particularly difficult to control. Chemically synthetized treatments are today the most effective methods to limit fungal diseases on apples but their application is more and more restrictive in conventional agriculture and prohibited in organic crops. Alternative methods are therefore needed to better control postharvest diseases and to mitigate the risks of high economical losses after harvest. In this study, we evaluated the effect of a gaseous ozone treatment applied during storage on two apple cultivars, ‘Topaz’ and ‘Otava’. Fruits were stored at 4 °C during 6 months and treated with gaseous ozone at different concentrations and frequencies of application. Development of rot and assessment of fruit quality in terms of firmness, total soluble solids, acidity and texture were evaluated. Results showed that ozone was effective to limit fungal growth, but not to stop it. Key fruit quality attributes were not altered by the treatments, but ozone application at high doses and frequencies induced the development of greasiness on ‘Topaz’ and lenticel breakdown on ‘Otava’. This study brings robust evidences that ozone is an interesting alternative method to limit fruit losses after harvest and that the dose and frequency of application are determinant for commercial fruit quality.