Background: The COVID-19 pandemic caused major shifts in students' learning strategies as well as teaching environments that profoundly affected the delivery of anatomy courses in medical schools. The Department of Anatomy at the University of Zagreb School of Medicine had a unique experience where the anatomy course in 2019/2020 was first taught in-person before transferring to an online course delivery, while the inverse happened in 2020/2021. The core curriculum, course material and examination criteria were the same in both academic years. The aim of the study was to determine whether course delivery affected students' perceptions of the course and whether it impacted students' engagement and success. Methods: The students' perceptions of the course were assessed via an anonymous course survey (student evaluation of teaching, SET). The questions in the SET assessed the usefulness of teaching modalities rather than students' satisfaction. Most questions were in the form of statements to which students responded with their level of agreement on a five-point Likert scale. Differences between responses in 2019/2020 and 2020/2021 were analyzed using the Mann-Whitney test. Effect size was estimated using Cliff's delta and association between responses was assessed using Spearman's r coefficient. Results: Students' perceptions were significantly affected by changes in course delivery. Students' success and engagement were higher in 2019/2020 when in-person teaching preceded online teaching. Furthermore, students' views on course organization and the usefulness of continuous assessment were more positive in 2019/2020. Finally, students' perceptions of the usefulness of online materials and activities were more positive in 2019/2020. All comparisons between the two academic years were statistically significant (P ≤ 0.0001 for all comparisons, Mann-Whitney test). Conclusions: Students' perceptions of the anatomy course were dependent on the teaching environment they were exposed to at the beginning of the course. A transfer from in-person to online course delivery was more successful than vice-versa. This has important implications for structuring hybrid courses in medical education in the future.