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While emotions are dynamic in nature, few studies have explored emotion dynamics in self-regulated learning (SRL). This study fills this gap by comparing the emotion dynamics across phases of SRL (i.e., forethought, performance, and reflection) in 47 medical students who are solving a virtual patient case. Students facial expressions and EDA were analyzed using recurrence quantification analysis. The results indicated that students were more likely to experience a sequence of repeating emotions and frequent skin conductance response in the performance phase of SRL. These findings highlight the temporal and dynamic nature of emotions in the process of SRL. The study has educational implications for instructors with respect to the usage of facial expressions and EDA in monitoring students’ emotions.