Rapid social change and the complexity of global challenges require educational institutions to not only develop the intellectual competencies of the younger generation but also to foster character, integrity, leadership, independence, and an entrepreneurial spirit. However, the integration of leadership and entrepreneurial values into the pesantren education system still requires more in-depth study, particularly regarding the forms of internalization and the practices used to cultivate these values in the lives of santri. This study aims to analyze the process of internalizing leadership and entrepreneurial values within the pesantren education system and to identify the forms of guidance applied in shaping students’ competencies and character. The study employs a qualitative approach using a case study design. Data were collected through observation, in-depth interviews, and document analysis, and were then analyzed through the stages of data reduction, data presentation, and the drawing and verification of conclusions. The research results show that the internalization of leadership and entrepreneurial values is carried out in an integrated manner through the formal curriculum, co-curricular activities, and extracurricular activities. Leadership values are developed through classroom learning, student organizations, the division of responsibilities, accountability mechanisms, deliberation, and character building. Meanwhile, entrepreneurial values are internalized through skills training and practice-based entrepreneurship programs that provide direct experience in developing independence, creativity, responsibility, and the ability to manage productive activities. These findings indicate that Islamic boarding schools not only function as institutions for transmitting Islamic knowledge but are also capable of building an educational ecosystem that integrates character building with the development of leadership and entrepreneurial capacities. The contribution of this research lies in reinforcing the perspective that the integration of Islamic education, leadership, and entrepreneurship through real-world learning experiences can serve as a strategy for nurturing students who are adaptable, independent, and prepared to face the dynamics of social life and the challenges of the future.