This is the first study to reveal potential markers for volatile changes during ambient and accelerated shelf life of pasteurized apple juice. The volatile changes were monitored at 20, 30 and 40 °C using a headspace solid-phase microextraction-gas chromatography-mass spectrometry fingerprinting method. Using modern chemometrics and feature selection, hexanal, trans-2-hexenal, dimethyl sulphide, furfural, ethyl acetate and 1-pentanol were chosen as potential shelf life markers. Volatiles associated with the green, grassy and fresh apple aroma, such as hexanal and trans-2-hexenal, decreased during storage, whereas thermal load and browning associated compounds, like dimethyl sulphide and furfural, increased during storage. Hexanal and trans-2-hexenal can be markers to monitor the change in green-apple like character. Furfural and dimethyl sulphide can be markers of temperature abuse during juice processing and storage. Furfural can also be an indicator for juice browning. The present work effectively identified potential markers to monitor and predict volatile aroma changes of shelf stable apple juice in different storage conditions. Sensory analysis can be conducted in the future to confirm the aroma relevance of selected markers.