Introduction This study aims to determine the effect of sudden changes in learning environments on students’ performance, in the context of the COVID-19 pandemic lockdown. We present an analysis of the kinesiology program, focusing on the learning modality changes through the years, and its impact on students’ performance. Methods We analyzed three periods over five years. During the Pre-pandemic period (2018-2019), classes had been taught in-person, during the pandemic (2020-2021) classes had been taught online, and during end of lockdown (2022) classes had return to in-person modality. In addition, we also examined the academic performance outcomes by gender during the three periods. Results We found that the academic performance significantly increased in all cohort of career, increasing the average grade from 4.7 ± 0.08 (2018 to 2019, in-person) to 5.15 ± 0.07 during the pandemic period, from 2020 to 2021, when online modality was utilized. Furthermore, when returning to in-person classes in 2022, the academic performance reduced significantly to 4.6 ± 0.17. We also found that gender did not have an influence on academic performance in any of the learning environments presented. However, during clinical internships, we found that gender had a significantly effect on academic performance. Conclusion Based on these results, we conclude that the sudden shift from in-person learning to online learning modality helped improved the learning performance of student, reflecting those results on better students’ performance scores that could be associated with the enhanced efficient use of time.