Team-based primary care has been shown to be an important initiative for transforming primary care to achieve whole-person care, enhance health equity, and reduce provider burnout. Organizational approaches have been explored to better implement team-based care but a thorough understanding of the role of system functions is lacking. We aimed to identify the combinations of system functionalities in primary care practices that most enable effective teamwork. We used a novel method, qualitative comparative analysis (QCA), to identify cross-case patterns in 19 primary care practices in the Harvard Academic Innovations Collaborative (AIC), an initiative for transforming primary care practices by establishing teams and implementing team-based care. QCA findings identified that primary care practices with strong team dynamics exhibited strengths in three operational care process functionalities, including management of abnormal test results, cancer screening and medication management for high-priority patients, care transitions, and in health information technology (HIT) functionality. HIT functionality alone was not sufficient to achieve the desired outcomes. System functionalities in a primary care practice that support physicians and their teams in identifying patients with urgent and complex acute illnesses requiring immediate response and care and overcoming barriers to collaboration within and across institutional settings, may be essential for sustaining strong team-based primary care.