Faith-based health promotion programs have been effective in increasing healthy eating (HE) and physical activity (PA). Very few reports exist regarding church leaders' anticipated and experienced barriers and facilitators to program implementation. Pastors (n = 38, 70%) and program coordinators (n = 54, 100%) from churches (N = 54) who attended a program training answered open-ended questions about anticipated barriers and facilitators to implementing the HE and PA parts of the Faith, Activity, and Nutrition (FAN) program. Twelve months later, pastors (n = 49, 92%) and coordinators (n = 53, 98%) answered analogous questions about their experienced barriers and facilitators to implementing the HE and PA parts of the FAN program. Responses were coded using thematic analysis. Similar themes appeared at baseline and follow-up for anticipated and experienced barriers and facilitators. The most common barriers were no anticipated barriers, resistance to change, church characteristics, and lack of participation/motivation. The most common facilitators were internal support, leadership, and communication. Few differences were found between anticipated and experienced barriers and facilitators. Understanding these perspectives, particularly overcoming resistance to change and church characteristics through strong leadership and internal support from church leaders, will improve future program development, resources, and technical assistance in faith-based and non-faith-based communities alike.