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A significant proportion of universities throughout the world switched from conventional face-to-face course delivery to emergency remote teaching (ERT) in response to the pervasive COVID-19 outbreak. A series of challenges are faced by both teachers and students as a result of the rapid and abrupt switch to ERT. Within the context of ERT, physics courses encounter certain challenges in contrast to certain liberal arts courses. In particular, this study sought to determine whether physics students and nonphysics students had diverse levels of flow experience and cognitive load when applying ERT during the global pandemic period. Furthermore, this study examined whether ERT for physics students varied depending on gender and educational level. Following the completion of their ERT courses at the end of both the Spring semester of 2020 and the Fall semester of 2022, a total of 1073 participants, including both physics majors and nonphysics majors, participated in our research. From the result, physics students had better performance in the flow experience encompassing its three constructs: enjoyment, engagement, and control. Physics students demonstrated a higher germane cognitive load and a lower extraneous cognitive load when compared to nonphysics students. Moreover, a considerably higher extraneous cognitive load was observed among male physics students than among their female counterparts during the ERT. Nonetheless, physics students at undergraduate and graduate levels did not significantly differ in their flow experiences or cognitive load. Overall, physics majors had a more positive perception of their ERT learning experience, and the impact of ERT on physics students was significantly less detrimental.