Organizational shadows refer to a set of informal relationships, hidden power dynamics, informal networks, unwritten norms, and undocumented practices that emerge alongside the formal organizational structure and may influence decision-making processes, resource allocation, information flows, organizational culture, and performance. The present study was conducted with the aim of developing a model for managing organizational shadows in the Endowments and Charity Organization. This qualitative study was conducted within a postmodern paradigm. Data were collected through in-depth, semi-structured interviews with academic experts in the fields of management and psychology, as well as organizational managers with managerial experience. Participants were selected through purposive and snowball sampling, and sampling continued until theoretical saturation was achieved. In total, 15 in-depth interviews were conducted with experts and managers. The collected data were analyzed using the Attride–Stirling thematic analysis method, through which open codes, basic themes, organizing themes, and global themes were identified and organized into a model for managing organizational shadows. The findings revealed that organizational shadows have a dual nature and, depending on how they are formed and managed, may generate negative consequences or constructive capacities for the organization. On the negative side, the identified components included hidden power, hidden control over resources, hidden influence on managerial decisions, backstage communications, alternative practices for formal decision-making, unwritten norms, belief in individuals and personal influence, undocumented values, and reduced transparency and access to information. Conversely, organizational shadows may contribute to organizational agility, learning, innovation, and resilience through increased flexibility and responsiveness, support for employee learning and development, and strengthening of internal support networks. Accordingly, managing organizational shadows does not mean eliminating informal relationships and structures; rather, it requires identifying, directing, and aligning their constructive capacities with the formal structure while controlling the adverse consequences of hidden concentrations of power and information. The resulting model can provide a basis for enhancing transparency, justice, trust, efficiency, and effectiveness in the Endowments and Charity Organization.