This article examines how philosophical values embedded in the pesantren tradition can be operationalised into a contextual anti-bullying program. Using a qualitative case study of Pesantren Nurul Yaqin (Indonesia), the study triangulates in-depth interviews with eight key participants (a pesantren leader, five educators, and two students), participatory observation, and document analysis. Data were analysed through iterative thematic coding. The findings suggest that bullying in pesantren is repeated peer aggression sustained by power imbalance. At the same time, severe incidents may be contained when a strong moral ecology regulates institutional life. At Pesantren Nurul Yaqin, four ideals such as tawadhu’, ukhuwah Islamiyah, silaturahim, and ihsan, function as moral anchors that restrain domination, strengthen belonging, and activate prosocial defending. However, the study also identifies the limits of informal norms; values may be unevenly applied and insufficient when victims hesitate to disclose harm. Accordingly, the article proposes a values-based, Whole-School Approach-aligned protocol that formalises local wisdom into safeguards, including a confidential reporting mechanism, a peer-inclusive anti-bullying team, staged restorative responses, educator role-modelling, and parent or community engagement.