<i>Background:</i> Different studies considered the mechanisms involved in the maintenance of binge eating in bulimia nervosa (BN) and binge eating disorder (BED), suggesting different pathways. The present 3-year follow-up study evaluated the relationships between psychopathological variables, and objective and subjective binge eating episodes in the two syndromes. <i>Methods:</i> 85 BN and 133 BED patients were studied. Objective and subjective binge eating, and psychopathological data were collected in a face-to-face interview, and by means of different self-reported questionnaires. The same assessment was repeated at baseline (T0), at the end of an individual cognitive-behavioral treatment (T1), and 3 years after the end of treatment (T2). <i>Results:</i> At baseline, BN and BED patients showed different emotions associated with binge eating: anger/frustration for BN and depression for BED patients. Objective binge eating frequency reduction across time was associated with lower impulsivity and shape concern in BN patients, and with lower emotional eating and depressive symptoms in BED patients. Lower subjective binge eating frequency at baseline predicted recovery, in both BN and BED patients. Recovery was associated with lower impulsivity and body shape concern at baseline for BN patients, and lower depression and emotional eating for BED patients. <i>Conclusions:</i> Eating psychopathology, psychiatric comorbidity, impulsivity and emotional eating have a different pattern of association with objective and subjective binge eating in BN and BED patients, and they act as different moderators of treatment. A different target of intervention for these two syndromes might be taken into account, and subjective binge eating deserves an accurate assessment.