Development of firm flesh browning, a physiological disorder, in ‘Empire’ apples during long term controlled atmosphere (CA) storage, can be enhanced by 1-methylcyclopropene (1-MCP), an inhibitor of ethylene perception. The disorder develops earlier in stem-end tissues than in calyx-end tissues. The antioxidant scavenging systems in the tissue zones of fruit stored under CA conditions (2 kPa O2/2 kPa CO2) at 3 °C at 6 and 10 months were investigated. Flesh tissue browning as indicated by lightness and hue angle was greater in 1-MCP treated than in untreated fruit, and in stem-end tissues than in calyx-end tissues. 1-MCP treatment decreased superoxide production as indicated by nitroblue tetrazolium (NBT) reducing activity but increased H2O2 concentrations, while treatment effects on malondialdehyde concentrations were inconsistent. Ascorbic acid (AsA) and glutathione (GSH) concentrations declined during storage, regardless of 1-MCP treatment, but were lower in stem-end tissue than in calyx-end tissue. While ascorbate peroxidase (APX) activity was not affected by 1-MCP treatment, its activity in untreated fruit was lower in stem-end tissues than in calyx-end tissues. The activities of superoxide dismutase (SOD) and copper/zinc-superoxide dismutase (Cu/Zn-SOD) increased during storage. The activities of catalase (CAT) and peroxidase (POX) decreased in 1-MCP treated fruit but effects on activities of other enzymes were inconsistent. Overall, higher browning may be associated with lower AsA and GSH concentrations in stem-end tissues, but the enhanced browning resulting from 1-MCP treatment does not appear to be directly related to antioxidant metabolism.