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Background: Schizophrenia is often characterized by a general disruption of self-processing and self-demarcation. Previous studies have shown that self-monitoring and sense of agency (SoA, i.e., the ability to recognize one's own actions correctly) are altered in schizophrenia patients. However, research findings are inconclusive in regards to how SoA alterations are linked to clinical symptoms and their severity, or cognitive factors. Methods: In a longitudinal study, we examined 161 first-episode schizophrenia patients and 154 controls with a continuous-report SoA task and a control task testing general cognitive/sensorimotor processes. Clinical symptoms were assessed with the Positive and Negative Syndrome Scale (PANSS). Results: In comparison to controls, patients performed worse in terms of recognition of self-produced movements even when controlling for confounding factors. Patients' SoA score correlated with the severity of PANSS-derived "Disorganized" symptoms and with a priori defined symptoms related to self-disturbances. In the follow-up, the changes in the two subscales were significantly associated with the change in SoA performance. Conclusion: We corroborated previous findings of altered SoA already in the early stage of schizophrenia. Decreased ability to recognize self-produced actions was associated with the severity of symptoms in two complementary domains: self-disturbances and disorganization. While the involvement of the former might indicate impairment in self-monitoring, the latter suggests the role of higher cognitive processes such as information updating or cognitive flexibility. The SoA alterations in schizophrenia are associated, at least partially, with the intensity of respective symptoms in a state-dependent manner.