The COVID-19 pandemic has led to significant re-organisation of healthcare delivery in hospitals, with repercussions on all professionals working in healthcare. We aimed to assess the impact of the pandemic on the mental health of professionals working in health care institutions and to identify individual and environmental factors influencing the risk of mental health disorders. From 4 June to 22 September 2020, a total of 4370 professionals responded to an online questionnaire evaluating psychological distress, severity of post-traumatic stress symptoms, stress factors, and coping strategies. About 57% of the professionals suffered from psychological distress, and 21% showed symptoms of potential post-traumatic stress. Professionals working in radiology, those working in quality/hygiene/security and nurses’ aides were the most affected groups. The media focus on the crisis, and a high workload were the most prevalent stress factors, followed by uncertainty regarding the possibility of containing the epidemic, the constantly changing hygiene recommendations/protocols, and the lack of personal protective equipment. The use of coping strategies, notably positive thinking, helped to mitigate the relation between perceived stress and mental health disorders. The COVID-19 pandemic has had far-reaching negative repercussions for all professionals, with some sectors more markedly affected. To prevent mental health disorders in professionals during a public health crisis, support services and management strategies within hospitals should take account of the importance of positive thinking and social support.