The COVID-19 pandemic affected the organization of health services and had consequences for health teams, according to the pre-existing safety and working conditions. During the first week of April 2020, a cross sectional study was carried out with a qualitative-quantitative approach. The aim was to explore the conditions determining the organizational climate: leadership, communication, institutional resources, cohesion/conflict management, and training; and how these were perceived by health personnel to deal with the pandemic. A total of 5670 healthcare workers participated in an online survey and 50 were interviewed, from all subsectors of the Argentinean health system (public, private and union-health insurance); 72.9% were women, 51.4% were physicians, and the predominant age group was under 40 years. In the qualitative sample (interviews), 52% were men, 62% were physicians, and the average age was 44.8 years. The dimensions of the organizational climate were stratified and five independent predictors of perception of conditions were identified: age, gender, tasks performed, health system subsector, and jurisdiction. The condition most frequently perceived as inadequate were the inaccessibility of institutional resources and the access to personal protective equipment was a major concern. Claims included the need of institutional strategies to support healthcare workers and of a clear and uniform communication. In conclusion, at the time of the study, the health personnel perceived serious deficits in their organizations regarding the conditions necessary to confront COVID-19, with differences among subsectors of the health system.