Virtual reality (VR) has been shown to induce excessive affective processing, which in turn impacts the learning process and learning outcomes. Therefore, a better understanding of emotional dynamics and how emotions are instigated while learning with VR is needed. For this purpose, the students learning process with a VR simulation was captured using continuous measurement of facial expressions. In addition, personality traits and self-regulated emotion (SRE) characteristics were examined. The findings suggest that overall, joy was the most predominant emotion expressed by students, while intraindividual components of personality traits and SRE strategies were associated with negative emotional expressions. Specifically, students with high conscientiousness or agreeableness personality traits tended to experience less anger and/or sadness. In addition, the findings demonstrate that the experience of these negative emotions was mediated by the SRE strategies of reappraisal and suppression, implying a mechanism of emotional engagement while learning with VR. This suggests that while individual personality traits are relatively stable and immutable, SRE preferences can be supported as part of the VR instructional design and scaffolding. Future studies should explore how students' emotion regulation preferences can be supported to benefit their emotional experiences while learning.