In urban South Africa, community-based social enterprises (CBSEs) face challenges at the intersection of financial and environmental sustainability and social purpose. These enterprises address social exclusion and community development within complex institutional environments. Despite increasing governmental support, CBSEs struggle with historical inequalities, resource limitations, high poverty levels, inadequate infrastructure, and complex social dynamics. These challenges contribute to a high failure rate among SMMEs, including CBSEs, which represent approximately 71% of community-level businesses. This study examines how complex system dynamics in marginalized South African suburbs impact the sustainable leadership and resilience of CBSEs. Utilizing a qualitative approach, the study conducted 15 in-depth semi-structured interviews with CBSE leaders. The findings revealed that effective leadership in CBSEs requires extraordinary abilities to traverse complexity, adapt to changes, and engage in dynamic organizational change. The key themes identified included adaptive and flexible leadership, interdependencies and network collaboration, community engagement and co-creation, continuous learning and feedback loops, policy influence and response, and resource utilization and constraints. By applying complex systems leadership theory (CSLT) and sustainable leadership principles, the research offers insights into the mechanisms enabling CBSEs to thrive in challenging environments. These findings contribute to Social Enterprise Management and Leadership Studies, providing practical implications for policymakers and practitioners to support CBSE development and sustainability in marginalized urban communities.