The present study evaluated the performance of some enzymatic and non-enzymatic antioxidant systems against oxidative stress for 10 to 30 d of refrigeration (R) and 15 to 50 d in controlled atmosphere (CA) conditions in both exocarp and mesocarp of Hass avocados from early and late harvests and at shelf life (SL) or consumption maturity. The possible relationship of the antioxidant systems with the occurrence of physiological disorders is also evaluated. The results indicate that the enzymatic system—superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), phenylalanine ammonium lyase (PAL) and polyphenoloxidase (PPO)—as well as the non-enzymatic system—such as phenolic compounds (PC)—showed different responses to the stress generated during storage and shelf life. In general, SOD, CAT, PAL and PPO did not significantly vary in storage (R or CA). At consumption maturity, SOD, POD and PAL activities decreased in the mesocarp (RSL and CASL), while CAT increased in the exocarp for CASL15-50d. PC instead decreased in the exocarp as the harvest period progressed while it increased in the mesocarp. Physiological disorders (dark spots) showed only in refrigeration on the exocarp at R30d and in mesocarp at RSL30d coincident with low SOD and low SOD and POD activity values, as well as low PC contents (p-coumaric and its derivatives and caffeic acid derivatives), respectively. The results support the use of CA as a postharvest technology to prevent the development of physiological disorders through the joint action of antioxidative defenses during avocado transport to distant markets until consumption maturity is reached.