Conflict Resolution Management (CRM) often becomes a burdensome necessity in academic institutions, where clashing interests, unequal resource distribution, and strained interpersonal dynamics undermine leadership and organizational stability. This study explored the CRM approaches of academic leaders in Higher Educational Institutions (HEIs) within the Davao Region, focusing on challenges, coping mechanisms, and insights. Anchored in the Thomas–Kilmann Conflict Mode Instrument (TKI), the study used an embedded multiple-case study design. Semi-structured interviews served as the primary data-gathering method. Findings revealed that leaders strategically applied the five conflict-handling styles: competing for urgent compliance, collaborating for inclusivity and trust, compromising for pragmatic middle-ground solutions, accommodating for preserving relationships, and avoiding for de-escalation. Challenges such as miscommunication, resistance to change, hierarchical power dynamics, and emotional strain highlight the complexity of institutional conflict. Coping strategies included emotional regulation, collective accountability, empathy, wellness initiatives, and peer consultation, which collectively support resilience and effectiveness. Insights emphasized the importance of flexibility, balancing results with relationships, and continuous growth through feedback. The results align with the TKI framework, confirming that no single style is universally effective. Instead, academic leaders adapt modes situationally, blending assertiveness with empathy to sustain institutional integrity and relational harmony. This study validates the TKI’s emphasis on flexibility and contextual application, underscoring that effective conflict management in higher education requires adaptive leadership, emotional intelligence, and a commitment to both organizational goals and human relationships.