The objective of this study was to evaluate the effects of extremely low oxygen partial pressure storage (ELO) maintained in static or dynamic controlled atmosphere monitored by chlorophyll fluorescence (DCA-CF) in the aerobic and anaerobic metabolism and its effects on physiological disorders and quality of ‘Royal Gala’ apples after 9 months, plus 7 days at 20 °C. Several static CA conditions were evaluated and compared to DCA-CF. Fruit stored under 0.4 kPa O2 + 1.0 kPa CO2 had similar quality maintenance as fruit stored under DCA-CF. Fruit stored under these two conditions were also healthier and had higher flesh firmness and lower flesh breakdown than CA-stored fruit. The partial pressure of oxygen (pO2) decreased to 0.15 kPa O2 + 0.0 kPa CO2 resulted in high anaerobic metabolism (acetaldehyde, ethanol, and ethyl acetate accumulation), which damaged fruit cells and led to low oxygen injury and consequently fewer healthy fruit amount.