Long-term storage of apples (Malus x domestica, Borkh.) is increasingly taking place under Dynamic Controlled Atmosphere (DCA). The oxygen level is lowered to ≤ 1 kPa O2 and the apples are stored just above the Lower Oxygen Limit (LOL). Low oxygen stress during controlled atmosphere storage can lead to fermentation in apples if oxygen levels are too low. Chlorophyll fluorescence can be used to detect low-oxygen stress at an early stage during storage. The currently available non-imaging fluorescence systems often use the minimal fluorescence (Fo) parameter. In contrast, the use of chlorophyll fluorescence kinetics is insufficiently described. Therefore, this study aimed to gain more knowledge about the response of chlorophyll fluorescence kinetics to low oxygen stress in apples using a fluorescence imaging system. The results show that the kinetic fluorescence curves differ under aerobic and fermentation conditions. The fermentative conditions initiated a decrease in fluorescence intensity upon application of the saturation pulses during exposure to actinic light. This result was made at 18 °C and 2 °C ambient temperatures. Interestingly, the kinetic curve changed at 2 °C before fermentation products accumulated in the apples. Non-photochemical quenching (NPQ) decreased under fermentation conditions in the dark phase after relaxation. Upon entering the dark relaxation phase after Kautsky induction, ɸPSII began to increase. Under atmospheric oxygen conditions, ɸPSII reached values of 0.81 to 0.76, while under fermentation, ɸPSII values ranged from 0.57 to 0.44.