This study examines the role of everyday and scientific concepts in developing student leadership in a self-access learning center (SALC) in Japan. For this purpose, data from three student learning community leaders and one SALC faculty member participating in an 18-month ethnographic case study of the Learning Group (LG), a student-led learning community within a university-based SALC in central Japan, was reexamined according to a framework informed by concept-based learning. Data was first coded inductively utilizing reflective thematic analysis (Braun & Clarke, 2006) and subsequently deductively using communities of practice theory and the themes of scientific and everyday knowledge. This data highlights numerous ways three leaders of the LG had internalized concepts introduced to them through a SALC-based leadership course administered by a learning advisor (LA) and how this influenced not only their individual learning trajectories, but also the path of their community. Furthermore, the LG leaders were able to develop coherent management/facilitation guidelines for themselves and for future generations of leaders from the social mediation that collaborative group reflection and intentional reflective dialogue afforded. The implications of this study highlight the potential value within SALCs of learning advisors engaging in concept-based instructional approaches where explicit instruction is internalized through dialogic and communicative verbalization and through finding avenues for learners to apply scientific concepts to everyday practice.