Systemic issues within and beyond organizations are a significant source of suffering for individuals, communities, and societies at large, motivating scholars and practitioners to better understand and promote flourishing. Existing approaches, however, are falling short off addressing the interconnected nature of these issues, focusing either on individual-level solutions or system-level change, but rarely connecting the individual and the system. In the current research, we hope to provide an integrative, transdisciplinary perspective to articulate intra-personal capacities that can help organizational agents address the systemic well-being crisis. To do so, we first propose a multi-level framework for understanding and intervening on well-being, emphasizing the role of “flourishing agents”, a step beyond organizational change agents, in an interconnected system of individuals, groups, organizations, and societies. We argue that the interconnectedness imply the possibility of “cycles of suffering”, which calls for new capacities to develop within the flourishing agents. Next, we draw from three ancient wisdom traditions—Christianity, Buddhism, and Stoicism— to suggest what types of ‘inner development’ may be needed for flourishing agents to transform suffering into flourishing. Our perspective creates a dialogue between contemporary sciences (psychological, organizational, and sustainability) and ancient wisdom traditions to demonstrate how the inner development of organizational agents, especially their abilities to engage with the inevitability of suffering, can act as a “deep leverage” to address the systemic well-being crisis. Our perspective highlights the relevance of the organizational context and a deeper integration with organizational sciences in the emerging field of transdisciplinary science on flourishing and sustainable development.