The hospital health care professionals are the front-line fighting COVID-19 considering they are responsible for all the care provided to patients. The purpose of this study was to determine the impact of COVID-19 at the hospital management level and, also, to understand how psychosocial environment, and satisfaction of Health Professionals were affected. A case study was performed in a Portuguese Hospital. Data were collected at one hospital under study at two different occasions: the first before the pandemic (November 2019) and the second almost two years after the pandemic started (November 2021). Regarding data collection, 37.0% of participants responded in the occasion 1 (n = 296) and 63.0% responded in the occasion 2 (n = 503). The instrument for the Assessment of Global Management of Health Organizations (AGMHO) consists of 39 items organized into six dimensions (Gaspar et al. in J Occup Environ Med 63: 581-587, 2021). Comparing timings pre and during pandemic COVID-19, it was found that the participants in the pre-COVID-19 era showed stronger organizational culture, higher quality of life, better psychosocial environment regarding content/leadership and higher job satisfaction when compared to the participants during pandemic COVID-19. On the other hand, participants in the second occasion were found to have higher psychosocial risks related to mental health when compared to participants in the pre-COVID-19 phase. We conclude that the professionals' perception of the different dimensions of the health organization worsened after 2 years of the pandemic. With special focus on psychosocial risks at work and relationship with leadership.