Purpose: The purpose of this study was to investigate the perspective of school personnel regarding the impact of social-ecological factors and to identify salient ways to support school personnel in sustaining Comprehensive School Physical Activity Programs. Methods: In this mixed-methods longitudinal study, stakeholders were surveyed at two points in time (n = 67) and interviewed in semistructured interviews (n = 41) using card sorting to understand the influence of social--ecological factors on Comprehensive School Physical Activity Programs sustainability. Results: Across time, the perceived influence of social--ecological levels varied considerably: individual, t(78.86) = -4.22, p < 0.001, d = 0.52, interpersonal, t(88.20) = -2.32, p = 0.023, d = 0.09, organizational, t(80.56) = -2.38, p = 0.02, d = 0.29, and the community factor, t(83.24) = -3.05, p = 0.003, d = 0.30. Stakeholders rated ecological levels from greatest to least influential as individual, organizational, interpersonal, community, and policy. Themes within levels provided a deeper understanding of these influences. Conclusion: To successfully sustain Comprehensive School Physical Activity Programs in schools, balanced support from all social-ecological levels may be needed.