The main objective of this paper is to understand and characterize the healthy work environment of organizations during the COVID-19 pandemic. The study was carried out in 2021 including organizations from different sectors at the national level and involved 460 participants, 50.3% of which were female. The workers’ ages ranged between 18 and 67 years, with a mean of 44 years and a standard deviation of 11.36. The Healthy Workplaces Ecosystems Tool was used. Data was collected online from professionals in the organizations who agreed to participate in the study. Our results show that organizational culture has a strong relationship with the other components of a healthy work environment. Values, policies, and practices related to leadership engagement and professional involvement are related to the psychosocial work environment, the physical work environment, the social responsibility, heath, and stress management resources. The results confirm that an organizational culture that values the well-being and health of the organization’s professionals has a positive relationship with the psychosocial environment, the physical environment, and the relationship with the community and has more resources for professionals’ health. It was also found that an organizational culture mediated by the psychosocial environment is associated with more effective stress management. Management can use this model and this tool for systemic assessment of healthy workplace ecosystems within organizations, thus contributing to continuous monitoring improvements, helping to face the challenges proposed by the Sustainable Development Goals of the United Nations’ 2030 Agenda, namely the SDG3, Good Health and Wellbeing and Decent Work; SDG5, Gender Equality; and SDG 10, Sustainable cities and communities.