Background Electronic health records (EHRs) have become ubiquitous in US office-based physician practices. However, the different ways in which users engage with EHRs remain poorly characterized. Objective The aim of this study is to explore EHR use phenotypes among ambulatory care physicians. Methods In this retrospective cohort analysis, we applied affinity propagation, an unsupervised clustering machine learning technique, to identify EHR user types among primary care physicians. Results We identified 4 distinct phenotype clusters generalized across internal medicine, family medicine, and pediatrics specialties. Total EHR use varied for physicians in 2 clusters with above-average ratios of work outside of scheduled hours. This finding suggested that one cluster of physicians may have worked outside of scheduled hours out of necessity, whereas the other preferred ad hoc work hours. The two remaining clusters represented physicians with below-average EHR time and physicians who spend the largest proportion of their EHR time on documentation. Conclusions These findings demonstrate the utility of cluster analysis for exploring EHR use phenotypes and may offer opportunities for interventions to improve interface design to better support users’ needs.