The COVID-19 pandemic forced many universities and colleges to rapidly adopt online course delivery. As with any new foray, realizing the optimal aspects of a course to change became incredibly important for course instructors. In this study, we used a particularly sensitive method, i.e. Q-methodology, to evaluate changes based on students’ perceptions from fall 2020 to winter 2021. Q-methodology is commonly used to uncover shared values, opinions, and preferences. Using Q-methodology, students participating in both semesters of an undergraduate anatomy and physiology course were surveyed in fall 2020 and winter 2021. The Q-sample included 44 statements. Data from fall 2020 were treated as the baseline and changes in students’ perceptions from 2020 to 2021 were assessed. In total, 31 students completed both fall 2020 and winter 2021 course evaluations. Three salient factors emerged from the fall 2020 evaluation: Overtaxed students, Solo Achievers, and In-Person Learners. At the baseline, students were concerned mostly about the delivery of the course, then the winter 2021 evaluation showed how they were adjusting to online learning. The longitudinal Q-study proved to be robust in identifying changes in perceptions. These granular findings indicate how students might differ in viewing and evaluating online courses. This methodology can be used in redesigning and restructuring different components of an online course in higher education settings.