Our objective was to compare the effects of controlled atmosphere (CA) and modified atmosphere packaging (MAP) on fruit quality, chilling injury (CI) and pro- and antioxidative systems in ‘Blackamber’ Japanese plums. Matured fruit were stored for 5 and 8 weeks at 0–1 °C in normal air, CA-1 (1% O2 + 3% CO2), CA-2 (2.5% O2 + 3% CO2) and MAP (~10% O2 and 3.8% CO2). CA was more effective than MAP in retention of flesh firmness and titratable acidity during cold storage. Fruit stored in CA-1 showed reduced CI and membrane lipid peroxidation after 5 and 8 weeks of cold storage. Low O2 atmospheres appeared to limit the generation of reactive oxygen species (ROS) and their efficient scavenging through the concerted action of superoxide dismutase and peroxidase. The role of ascorbate–glutathione (AsA–GSH) cycle in the regulation of oxidative stress was also studied during and after storage in different atmospheres. In conclusion, optimum CA conditions delayed fruit ripening and CI through augmentation of antioxidative metabolism and suppression of oxidative processes.