Background: Health professionals are at high risk of poor mental health and well-being. Faced with this challenge, healthcare organizations must be healthy and safe work environments. Objectives: This study aims to take an in-depth, systemic look at whether healthcare organizations are healthy workplaces. Methods: The study involved 2190 participants aged between 19 and 71 (M = 44.73, SD = 10.29) and data were collected in 12 public hospitals between November 2021 and December 2023. The study used the Ecosystems of Healthy Workplaces instrument, which consists of a total of 62 items organized into nine dimensions based on the Healthy Workplaces model proposed by the World Health Organization. Results: Most dimensions revealed a moderate risk in terms of whether they were healthy work environments, while the dimension that revealed a high risk was related to psychosocial risks at work in relation to well-being and mental health. A total of 87% of the professionals reported at least one symptom of burnout and 61.4% reported having all three symptoms of burnout. Additionally, 25.4% reported having been victims of harassment at work. When comparing the groups, we identified that the higher risk groups were namely women, generation Z and X professionals, doctors (compared to the different professional groups under analysis such as nurses, operational assistants, psychologists, administrators, senior technicians, and managers), professionals with chronic illnesses, and those who reported harassment at work. Conclusions: We conclude that the work environment must be understood ecologically, by analyzing the different systems and their relationships. This makes it possible to identify priority factors and groups for intervention.