COVID-19 is a well-known respiratory disease spreading worldwide since January 2020, causing many deaths and massive pressure on health systems. This pandemic’s appearance compromised the health services’ sustainability and quality as many procedures were postponed or even canceled out, with an expected increase of adverse events like nosocomial infections, in-hospital deaths, and the worsening of the patients’ clinical status. Therefore, assessing whether the healthcare providers’ performance has changed is paramount. In this case, we evaluated the public hospitals in Portugal as the leading secondary health care providers in the country, which in turn has been highly affected by the pandemic. To this end, we developed a network Data Envelopment Analysis model serially relating efficiency and effectiveness. Using 2,795 observations from public hospitals and 18 variables, we observed consistent drops in efficiency when the pandemic started, followed by a recovery to levels above the pre-pandemic ones. Regarding effectiveness, we observed a positive trend during the evaluated period. In short, these results allow us to conclude that, apart from the great resilience of public healthcare providers, the Portuguese State was not prepared for a pandemic like COVID-19, but still the actions taken (including massive vaccination) were beneficial.