ABSTRACTApple juice flavor fractions were collected at several stages during a commercial process. Replicated experiments were designed to collect samples from untreated pulp, from enzyme treated pulp, after pectinase treatment, after microfiltration (MF), and after pasteurization. Additional juice heating experiments were carried out. Six apple juice flavor compounds were identified based on to retention times and reported studies. The flavor profile changed at the different stages of the production line. Temperatures used (∼57.2°C) for enzyme activation and MF tended to increase flavor compounds in apple juice except iso‐butyl acetate. The higher temperatures used (∼85°C) for pasteurization decreased all flavor compounds except propyl butyrate which increased. Results indicate apple juice may contain heat activated precursors of identified flavor compounds.