The reuse of healthcare data for various purposes will become increasingly important in the future. To enable the reuse of clinical data, structured and standardized documentation is conditional. However, the primary purpose of clinical documentation is to support high-quality patient care. Therefore, this study investigated the effect of increased structured and standardized documentation on the quality of notes in the Electronic Health Record. A multicenter, retrospective design was used to assess the difference in note quality between 144 unstructured and 144 structured notes. Independent reviewers measured note quality by scoring the notes with the Qnote instrument. This instrument rates all note elements independently using and results in a grand mean score on a 0–100 scale. The mean quality score for unstructured notes was 64.35 (95% CI 61.30–67.35). Structured and standardized documentation improved the Qnote quality score to 77.2 (95% CI 74.18–80.21), a 12.8 point difference (p < 0.001). Furthermore, results showed that structured notes were significantly longer than unstructured notes. Nevertheless, structured notes were more clear and concise. Structured documentation led to a significant increase in note quality. Moreover, considering the benefits of structured data recording in terms of data reuse, implementing structured and standardized documentation into the EHR is recommended.