To date, COVID-19 is by far the most impactful contagious disease of the 21st century and it has had a devastating effect on public health in countries around the globe. Elective medical services have declined markedly since the outbreak of the COVID-19 pandemic. Few studies have compared changes in healthcare quality before and during the outbreak of COVID-19 in Eastern Asian countries. We aimed to explore the impacts of COVID-19 on healthcare quality among medical centers in Taiwan. This was a retrospective study that collected anonymized data from the Taiwan Clinical Performance Indicator system, which was founded by the Joint Commission of Taiwan, an organization to promote, execute, and certify the nation’s healthcare quality policies. We explored quality indicators reported by more than three-quarters of medical centers in Taiwan from January 2019 to December 2020. The year 2019 was defined as the baseline period and 2020 was defined as the period after the start of the outbreak of COVID-19. Quality indicators from different regions were analyzed. Unscheduled returns of emergency patients within 72 h of their discharge, unscheduled returns of hospitalized patients within 14 days of their discharge, and unscheduled returns of surgical patients to the operating room during hospitalization all declined during the COVID-19 outbreak. Interestingly, the proportion of acute ischemic stroke patients receiving intravenous tissue-type plasminogen activator (IV-tPA) increased during outbreak of COVID-19. There were significant regional variations in healthcare quality indicators among medical centers in northern and middle/southern Taiwan. The outbreak of COVID-19 changed different patterns of healthcare systems. Although healthcare quality seemed to improve, further investigation is warranted to better understand whether those who were in need of returning to the emergency room or hospital were reluctant or were prevented from travel by the shelter-in-place policy.