Objective Healthcare systems around the world face a turbulent and unstable global and local ecosystem that changes daily and impacts the healthcare organization and its workforce. This challenging environment, coupled with economic pressures, is forcing healthcare systems to change and adopt strategic and technological processes to adapt to change at all levels of the system (macro-holistic multi-systemic, mezzo-organizational, and micro-personal). Methods In this study, through 32 in-depth, semi-structured interviews with healthcare professionals working in public general hospitals in central Israel, we examined, mapped, and highlighted the conflicts and moral dilemmas they have faced in recent years, alongside the processes of strategic, technological, and digital changes that the healthcare system has undergone. Results The findings from both a categorical–deductive approach and an inductive approach analysis reveals four main themes: innovation paradox, quality and treatment conflict, information and knowledge conflict, and personal needs and values. The themes and sub-themes are sorted across the three levels of the healthcare system. Conclusions These findings represent a wide range of conflicts and moral dilemmas that arise from the implementation of strategic change and digital transformation, adding to the already numerous ethical issues and moral dilemmas in healthcare and bioethics that are associated with three levels of the system. These challenges and moral conflicts can be barriers to implementing the necessary changes, as well as challenging individuals’ internal values, potentially leading to burnout and moral distress. Given the importance of this issue and the intensification of change processes over the next few years, it is up to the management and key stakeholders to implement these processes in a way that addresses the conflicts and challenges that health professionals face. Minimizing the level of challenges and moral distress in the health sector will be to the benefit of the system, its workers, and the patients it serves.