Background: This paper presents the effectiveness of a multi-component elementary school-based nutrition education program, the Integrated Nutrition Education Program (INEP), which has been in existence for over 25 years. INEP includes components to address multiple layers of influence: hands-on nutrition education lessons in the classroom (student-level), parent education, and outreach (home-level), and facilitation of a planning process to implement policy, system, and environmental (PSE) school changes (school-level). Methods: Three evaluation tools assessed the effectiveness of the program--(1) classroom plate waste measurement in intervention (N = 149 students) and demographically-matched comparison schools (N = 131 students), (2) pre/post classroom surveys completed by students who participated in INEP (N = 204), and (3) PSE change data from participating schools (N = 47 schools). Results: Students who participated in the nutrition education program were more likely to consume vegetable-based recipes and vegetables included in classroom nutrition lessons compared to students in comparison classrooms (Chinese vegetable salad: p < 0.001; couscous salad: p < 0.001; snap peas: p = 0.001). Classroom survey analyses showed improvements in student self-efficacy (p < 0.001), preference for vegetables (p = 0.005), and knowledge (p < 0.001). In addition, through a wellness planning process, schools implemented an average of 3.7 PSE changes per school. Conclusions: Results demonstrate a multi-component school-based nutrition education program improves student nutrition-related outcomes.