Structural and functional brain alterations as well as cognitive deficits are well-documented findings in schizophrenia patients. Cognitive impairments affect the long-term outcome of schizophrenia and are the main contributors to disability. Despite their clinical impact, however, no effective options are available to treat them sufficiently. Aerobic endurance training has been shown to have effects on brain plasticity, gray and white matter volume as well as functional connectivity measures and on cognitive functioning in animal models and healthy humans. However, effects of physical exercise in combination in combination with cognitive remediation are unknown in Schizophrenia. 21 chronic schizophrenia patients and 21 age and gender–matched healthy controls underwent 3 months of aerobic exercise (endurance training, 30 min, 3 times per week). 21 additionally recruited schizophrenia patients played table soccer (known as “foosball” in the USA) over the same period. After 6 weeks of endurance training or table soccer, all participants commenced standardized cognitive training with a computer-assisted training program. We could show that a 3-month endurance-training program combined with CR therapy had positive effects on everyday functioning in multi-episode Schizophrenia patients. Deficits improved from medium to mild as assessed with the GAF. Negative symptoms, short and long-term verbal memory and cognitive flexibility also improved with training. We could demonstrate grey matter volume increase in the left temporal lobe in schizophrenia patients undergoing endurance training. A non-endurance and coordinative training stimulus like playing table soccer led to a clearly distinct pattern of grey matter alterations in Schizophrenia patients.