Abstract: Patients with Schizophrenia Spectrum Disorders (SSD) often lead unhealthy lifestyles. This pragmatic trial evaluated the effectiveness of a lifestyle intervention, consisting of a 12-week aerobic exercise program and behavioural counselling, in SSD outpatients with metabolic syndrome (MetS). It also aimed to assess persistence of potential effects in a 24-month long-term follow-up. Effectiveness was measured in terms of a wide range of outcomes involving physical and psychological health, quality of life, physical activity and changes in motivation to exercise within the context of the self-determination theory. Our primary outcome was waist circumference change. Thirty-three out of 48 participants completed the study. No differences between groups were found in terms of BMI change or other metabolic parameters. However, the active group (AG) showed improvement regarding waist circumference, negative symptomatology and identified motivation to exercise during the study and follow-up. The AG exhibited changes toward a more active pattern of activity after intervention. Moreover, belonging to the AG was a significant predictor for achieving any degree of clinical improvement after 24-month follow-up. Combined interventions of exercise and behavioural counselling in SSD patients with MetS should be considered as an essential part of the integral treatment in the context of mental health services