The purpose of this study was to compare the effects of three different physical exercise programs on the symptomatology, body composition, physical activity, physical fitness, and quality of life of individuals with schizophrenia. A total of 432 patients were assessed for eligibility and 86 were randomized into the aerobic (n = 28), strength (n = 29) or mixed (n = 29) groups. Positive, negative, and general symptoms of psychosis, body mass index (BMI), physical activity (IPAQ-SF), physical fitness (6-min walk test [6MWT] and hand-grip strength [HGS]), and quality of life (WHOQUOL-BREF) were assessed at baseline, post-intervention (16 weeks), and at 10-months. Our results at 16 weeks showed significant improvements in all three groups in the negative, general, and total symptoms with moderate to large effect sizes (P < 0.01, ηp2 > 0.11), no change in the BMI, 6MWT or IPAQ-SF, and a significant improvement in the HGS test in the strength and mixed groups (P ≤ 0.05, ηp2 > 0.08). Nonetheless, all the improvements had disappeared at 10 months. We concluded that 3 weekly sessions of a moderate to vigorous progressive exercise program for 16 weeks improved the symptomatology of individuals with schizophrenia in all three groups, with no differences between them. However, the effects had declined to baseline levels by the 10-month follow-up, suggesting that exercise interventions should be maintained over time.