Background: Changing "Policy, System, and Environmental" features focused on physical activity and healthy eating behaviors can play a key role in obesity prevention strategies in early childhood education settings because of their broad reach and because they can be sustained over time. The primary aims of this study were to examine the implementation and sustainability of health-promoting PSE changes after facilitation of an innovative strategic planning process in child care settings. Methods: The evidence-based policy, system, and environment change process is a strategic planning tool derived from intervention mapping that involves convening interdisciplinary wellness teams at child care settings to implement healthy eating and physical activity-related policy changes. The process was conducted with 43 wellness teams representing 68 child care centers. Results: The average number of health-promoting evidence-based changes implemented across all child care centers was 5.07; the most common type of changes were environment changes. Overall, 42% of changes were partially implemented and 47% of changes were fully implemented at 6 months. Head Start wellness teams implemented 1.52 fewer health-promoting changes compared to private fee-based wellness teams (p < 0.05). Conclusions: Identifying health-promoting policy, system and environment changes that are most readily implemented and sustained in child care centers can inform systems-level interventions and resource allocation related to early childhood obesity. This strategic planning process is a successful tool to translate sustainable changes related to healthy eating and physical activity, improve the quality rating of diverse child care centers, and promote healthy behaviors in early childhood.