Islamic boarding schools (pesantren) as Islamic educational institutions not only function as centers for the transmission of knowledge and the formation of religious character, but also as social institutions that experience internal conflict dynamics. Differences in interests, leadership structures, and social relations among boarding school members have the potential to affect the stability and sustainability of the educational process. Previous research on Islamic boarding school conflicts generally places conflict within the framework of organizational management and social relations, thus tending to separate empirical analysis of conflict from the ethical-theological foundations of the Qur'an. Furthermore, studies that specifically operationalize the value of ishl?? in QS. Al-?ujur?t [49]: 9–10 as a framework for analyzing Islamic boarding school conflicts based on case studies are still very limited. Departing from this gap, this article aims to analyze the dynamics of Islamic boarding school conflicts through a qualitative approach using a case study method in one Islamic boarding school in Yogyakarta (identity disguised). Data were obtained through in-depth interviews, observations, and documentation studies. The results of the study indicate that Islamic boarding school conflicts arise in the form of leadership conflicts, structural conflicts between managers, and relational conflicts between students who are administrators and non-administrators. The findings of this study confirm that the values ??of ishl??, justice, and ukhuwah in QS. Al-?ujur?t [49]: 9–10 are not only normative, but can also be operationalized as an ethical-social framework in managing Islamic boarding school conflicts constructively.