COVID-19 is a disease caused by SARS-CoV-2, which has spread worldwide since the beginning of 2020. Several pharmaceutical and non-pharmaceutical strategies were proposed to contain the virus, including vaccination and lockdowns. One of the consequences of the pandemic was the denial or delay of access to convenient healthcare services, but also potentially the increase in adverse events within those services, like the number of hospital infections. Therefore, the main question here is about what happened to the performance of Portuguese public hospitals. The main goal of this work was to test if the Portuguese public hospitals’ performance has been affected by the SARS-CoV-2 pandemic. We used the Benefit-of-Doubt method integrated with the Malmquist Index to analyze the performance evolution over time. Then, we employed a multiple regression model to test whether some pandemic-related variables could explain the performance results. We considered a database of 40 Portuguese public hospitals evaluated from January 2017 to May 2022. The period 2017 to 2019 corresponds to the baseline (pre-pandemic), against which the remaining period will be compared (during the pandemic). We also considered fourteen variables characterizing hospital quality, divided into three main performance definitions (efficiency and productivity; access; safety and care appropriateness). As potential explanatory variables, we consider seven dimensions, including vaccination rate and the need for intensive care for COVID-19-infected people. The results suggest that COVID-19 pandemic features help explain the drop in access after 2020, but not the evolution of safety and appropriateness of care, which surprisingly increased the whole time.