Coronavirus disease 2019 (COVID-19) has heavily impacted medical clinical education in Taiwan. Medical curricula have been altered to minimize exposure and limit transmission. This study investigated the effect of COVID-19 on Taiwanese medical students' clinical performance using online standardized evaluation systems and explored the factors influencing medical education during the pandemic. Medical students were scored from 0 to 100 based on their clinical performance from 1/1/2018 to 6/31/2021. The students were placed into pre-COVID-19 (before 2/1/2020) and midst-COVID-19 (on and after 2/1/2020) groups. Each group was further categorized into COVID-19-affected specialties (pulmonary, infectious, and emergency medicine) and other specialties. Generalized estimating equations (GEEs) were used to compare and examine the effects of relevant variables on student performance. In total, 16,944 clinical scores were obtained for COVID-19-affected specialties and other specialties. For the COVID-19-affected specialties, the midst-COVID-19 score (88.513.52) was significantly lower than the pre-COVID-19 score (90.143.55) (P<0.0001). For the other specialties, the midst-COVID-19 score (88.323.68) was also significantly lower than the pre-COVID-19 score (90.063.58) (P<0.0001). There were 1,322 students (837 males and 485 females). Male students had significantly lower scores than female students (89.333.68 vs. 89.993.66, P=0.0017). GEE analysis revealed that the COVID-19 pandemic (unstandardized beta coefficient=-1.99, standard error [SE]=0.13, P<0.0001), COVID-19-affected specialties (B=0.26, SE=0.11, P=0.0184), female students (B=1.10, SE=0.20, P<0.0001), and female attending physicians (B=-0.19, SE=0.08, P=0.0145) were independently associated with students' scores. COVID-19 negatively impacted medical students' clinical performance, regardless of their specialty. Female students outperformed male students, irrespective of the pandemic.