This study investigates the physiological basis of effects of skin conductance biofeedback on anxiety disorders, depressive disorders and stress in drug-resistant temporal lobe epilepsy (TLE). This method presents an interest in seizure reduction and improvement in psychiatric comorbidities frequently associated with TLE. Our goal was to better understand the impact of biofeedback on seizure control and on emotional regulation. Fifteen patients with TLE were treated with 12 skin conductance biofeedback sessions and compared with 15 control TLE patients on a waiting list. They were evaluated in terms of seizure frequency, clinical evaluations of anxiety and depression and skin conductance responses (SCR) to five emotions: fear, disgust, sadness, happiness and peacefulness induced by short films. Biofeedback training significantly reduced seizure frequency with a mean reduction of -47.42% in the biofeedback group, while the control group did not differ at the two time measures. A significant improvement was found for depression and trait-anxiety in the biofeedback group but not in the control group. There were no differences on SCR on any emotion after biofeedback treatment. A correlation was found between mean change in SCR over the biofeedback treatment and the reduction of seizure frequency, but not between SCR changes and scores on psychiatric comorbidities. These results show independent effect of biofeedback on mood and seizure control. Improvements in anxiety and depressive symptoms were not related to SCR, whereas improved seizure control was, suggesting differential mechanisms underlying these two phenomena.