The COVID-19 pandemic has greatly affected higher education, but when learning shifted to an online environment it provided an opportunity to gain insight into how classroom format influences student performance and preferences. Thus, our objective was to assess student performance across classroom types, along with student perceptions of learning, to better understand the learning environment at the height of COVID-19. We evaluated student performance by final grade in undergraduate animal genetics (ANEQ 328) and large animal physiology (ANEQ 305) courses across four semesters, from before the pandemic through the return to in-person learning. In addition, students received surveys with questions regarding their learning experience. Survey analysis showed a consistent influence of COVID-19 within the classroom, mostly due to secondary effects. Student performance increased (P < 0.05) or was maintained in the pandemic centered semesters compared to pre-pandemic scores. When in-person learning resumed, scores in the ANEQ 305 course were worse (P < 0.05) than any previous semester but scores in the ANEQ 328 course returned to pre-pandemic levels. Overall, this study indicated that student performance was not negatively affected by the online transition during COVID-19 in these two courses, but it did decrease student satisfaction with their learning.