Background Physicians are hesitant to forgo the opportunity of entering unstructured clinical notes for structured data entry in electronic health records. Does free text increase informational value in comparison with structured data? Objective This study aims to compare information from unstructured text-based chief complaints harvested and processed by a natural language processing (NLP) algorithm with clinician-entered structured diagnoses in terms of their potential utility for automated improvement of patient workflows. Methods Electronic health records of 293,298 patient visits at the emergency department of a Swiss university hospital from January 2014 to October 2021 were analyzed. Using emergency department overcrowding as a case in point, we compared supervised NLP-based keyword dictionaries of symptom clusters from unstructured clinical notes and clinician-entered chief complaints from a structured drop-down menu with the following 2 outcomes: hospitalization and high Emergency Severity Index (ESI) score. Results Of 12 symptom clusters, the NLP cluster was substantial in predicting hospitalization in 11 (92%) clusters; 8 (67%) clusters remained significant even after controlling for the cluster of clinician-determined chief complaints in the model. All 12 NLP symptom clusters were significant in predicting a low ESI score, of which 9 (75%) remained significant when controlling for clinician-determined chief complaints. The correlation between NLP clusters and chief complaints was low (r=−0.04 to 0.6), indicating complementarity of information. Conclusions The NLP-derived features and clinicians’ knowledge were complementary in explaining patient outcome heterogeneity. They can provide an efficient approach to patient flow management, for example, in an emergency medicine setting. We further demonstrated the feasibility of creating extensive and precise keyword dictionaries with NLP by medical experts without requiring programming knowledge. Using the dictionary, we could classify short and unstructured clinical texts into diagnostic categories defined by the clinician.