Nutrition problems among primary school children increase the risk of illness, reduce school attendance, and impair academic performance. The Indonesian national school feeding program (ProGAS—Program Gizi Anak Sekolah) was developed to address these issues through the provision of healthy breakfast, nutrition education, and character building. This study employed a mixed-methods design involving 454 primary school students aged 8–14 years from 24 schools across four provinces. Data collection included structured questionnaires, 24 h dietary recalls, and anthropometric measurements. In-depth interviews with school principals, teachers, cooking teams, parents, students, nutritionists, and district education office staff were conducted to capture experiences and opinions on the ProGAS implementation. ProGAS significantly improved students’ dietary diversity, meal frequency, handwashing with soap, and nutrition knowledge, alongside a positive trend in school attendance. Improvements included higher mean dietary diversity, increased proportion of students eating ≥3 meals/day, greater correct responses on balanced nutrition, and higher rates of handwashing before meals (all < 0.01). Children also developed positive behaviors such as praying before meals, queuing, and taking responsibility for cleaning dishes. However, students’ breakfast habits did not significantly improve, the delivery of nutrition education was suboptimal, and no significant changes were observed in nutrient intakes or nutritional status based on BMI-for-age. While the energy and protein contributions of the ProGAS menu met the recommended 25–30% of daily requirements for breakfast, its micronutrient contributions remained below the recommended levels. Key management gaps include the delivery of nutrition education to students and the monitoring of implementation by local and national authorities. ProGAS demonstrated positive impacts on some dietary and hygiene practices as well as learning environment. To achieve greater improvements in breakfast habits, nutrient intake and nutritional status, it is recommended to strengthen the school feeding menus not only for dietary diversity but also for nutrient density, enhance capacity building for teachers, deliver regular and engaging nutrition education, and reinforce program monitoring.