The research into emotional regulation in eating disorders (EDs) has shown specific impairments and maladaptive coping strategies in patients, and there is an increasing interest in the role of the emotional domain in the treatment outcome. This study aims to evaluate the effect of a specialized inpatient treatment characterized by both an intensive and comprehensive standardized multidisciplinary programme based on cognitive-behavioural therapy and a flexible and personalized component implemented by third-wave interventions. A cohort of 67 female ED patients (anorexia nervosa = 28, bulimia nervosa = 28 and binge eating disorder = 11) underwent an evaluation of emotional regulation difficulties, alexithymia and dissociative symptomatology at admission to a specialized ED ward. The psychological modifications were subsequently re-evaluated upon discharge, after an inpatients treatment of 60 days, examining specific changes in the specific psychopathology. A significant improvement after specialized ED treatment was shown in alexithymia, emotional regulation difficulties and dissociation symptoms, with higher effect sizes in patients with higher alexithymia scores. As regards the specific effect of the psychological improvement, changes into alexithymia scores have shown specific correlations with ED psychopathology (p < 0.010) and with difficulties in emotional regulation (p < 0.010) in patients with higher alexithymia levels at admission. Emotional regulation and dissociation should therefore be evaluated in ED patients and may be improved with specific therapeutic approaches, while alexithymia remains a clinical trait, even with a significant reduction.