COVID-19 is a well-known respiratory disease that has spread worldwide since January 2020, causing many deaths and massive pressure on health systems. This pandemic’s appearance compromised health service sustainability and quality as many procedures were postponed or canceled, with an expected increase of adverse events like nosocomial infections, in-hospital deaths, and the worsening of the patient’s clinical status. For instance, the year 2020 featured an increase in undesirable results in Portugal: a rise of 10% in delayed first medical appointments, 0.02% in avoidable bloodstream infections, and more than 100 post-operative pulmonary embolisms and septicemia cases per 100,000 inpatients. Therefore, assessing whether the healthcare providers’ performance has changed is paramount. In this case, we evaluated public hospitals in Portugal. To this end, we developed a network data envelopment analysis model relating to efficiency and effectiveness. 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. We conclude that, apart from the great resilience of public healthcare providers, the Portuguese state was unprepared for a pandemic like COVID-19, but still the actions taken (including massive vaccination) were beneficial.