Background: The institutionalization of educational values is important for shaping organizational culture, leadership, and inclusive governance in Islamic educational institutions. The Nine Main Values of Gus Dur (SNUGD) emphasize justice, equality, humanism, and openness. Yet, limited empirical research has examined their institutionalization in Islamic primary education. Aims: This study examines how SNUGD is internalized and implemented through institutional management and explores how leadership transforms these ideas into organizational practices. Methods: A qualitative case study was conducted at Madrasah Ibtida’iyah Unggulan Miftahul Hikmah. Data were collected through semi-structured interviews, direct observations, and institutional documentation. Triangulation was employed to enhance credibility. Data were analyzed thematically through condensation, categorization, interpretation, and cross-source comparison. Results: The findings indicate that the internalization of Gus Dur’s ideas was highly effective, driven by the principal’s strong commitment and leadership. The process was reinforced by the participation of Alissa Wahid, Gus Dur’s daughter and SNUGD representative, in an event in Surabaya in 2014. Consequently, the school’s organizational culture became deeply embedded with values of justice, equality, humanism, and openness. These values were supported by measurable planning, structured implementation, and periodic evaluation. Conclusions: Based on these findings, it can be concluded that systematic management of SNUGD, supported by strong leadership commitment, fosters a rahmatan lil-'alamin orientation characterized by cooperation, equality, justice, humanism, and openness. The findings contribute empirical evidence on ideological institutionalization through educational leadership and reinforce the relevance of ideological hegemony theory in education and management.