Objectives  Exposure is regarded to be a crucial component of therapies for phobias. According to emotional processing theory, the success of exposure therapy is predicted by activation of subjective and physiological fear responses and their within-session habituation and between-session adaptation. This study tested this prediction for aviophobia. Methods  Seventy-nine participants following a highly standardized treatment program for aviophobia provided self-reported and physiological (heart rate, respiratory sinus arrhythmia and pre-ejection period) measurements of fear activation, within-session habituation, and between-session adaptation during exposure to flight-related stimuli, a flight simulator, and during two real flights. Multiple regression analyses were conducted to examine whether these measurements predicted therapy outcome up to 3 years after finishing therapy, including number of flights flown in this period. Results  Both subjective and physiological arousal measurements indicated strong fear activation and large within-session habituation and between-session adaptation during exposure. Flight anxiety measures showed large improvements up to 3 years after treatment (η2 between 0.72 and 0.91). Lower self-reported anxiety during flight exposure was associated with lower flight anxiety after exposure (R2 = 0.15) and more flights flown (R2 = 0.14). Within-flight habituation or between-session adaptation of self-reported anxiety had no relationship with treatment outcome. Within-flight habituation of HR reactivity (R2 = 0.10) and respiratory sinus arrhythmia reactivity (R2 = 0.11) was associated with lower flight anxiety directly after the flight, but not on flight anxiety 3 years after finishing therapy or on long-term flying behavior. Conclusions  The results provide only weak support for emotional processing theory. Low self-reported anxiety during in vivo flight exposure was the best predictor of successful long-term therapy outcome.