Recently there is a growing interest in the interaction of schizophrenia spectrum disorders (SSD) and substance use disorders (SUD), a condition named dual schizophrenia spectrum disorders (SSD+). While previous research has focused on clinical and cognitive aspects, little is known about the impact of comorbidity in the brain structure and functions. Evidence suggests that dual diagnosis patients, including SSD+, show a better neurocognitive functioning during the first years of illness, followed by a serious long-term decline. The initial search retrieved 94 articles, 12 were excluded for being redundant and 49 for not fulfilling the selection criteria. Thirty-three structural and functional neuroimaging studies that compare SSD and SSD+ patients were included. Both groups exhibited more brain alterations, in comparison to only SUD patients and healthy controls. SSD+ patients are less cognitively and emotionally impaired than non-dual SSD, but worse than healthy controls. The neurobiological alterations are prominent in SSD+ after five years of illness or longer. Moreover, SUD characteristics are important modulating factors, contrary to clinical severity or specific SSD diagnosis.